Smogon Tiering Philosophy
In my opinion, an effective tiering philosphy should be objective, consistent, clear, and simple. The Smogon mantra, summed up, is to tier Pokemon (
not moves, items, or abilities), which does a good job of fulfilling those criteria.
From a casual perspective, Pokemon are literally what the games are about, and using your favourites is a large appeal. Tiering by Pokemon plays into this idea ("there's always a tier where your favourite is viable!"), but is also reasonable from a more neutral standpoint because Pokemon are the fundamental building blocks of creating a team. What is a Pokemon though? From a competitive lens, Pokemon are primarily a typing and set of base stats (which are fixed), but also have a pool of moves and abilities to choose from (which are usually variable, except on Pokemon with one ability). Items are in general available to be held and usable, though some items having its effect limited depending on the holder. When you use a move, item, or ability, you do so within the context of using it on a particular Pokemon, even though generally they are not exclusive to that Pokemon. When you use a particular Pokemon, the moves, item, and ability can vary, even within the same "set" (with distinct sets being difficult to clearly define).
Pokemon
are clearly distinct from each other, though (with the exception of formes, which are sometimes tiered separately or not depending on their differences): if you ban a Pokemon, this has no
direct effect on any other Pokemon, i.e. they can still use the same sets, though obviously it could have an
indirect effect due to their effectiveness changing as a result of the ban. On the other hand, if you ban an item, move, or ability, then that has a
direct effect on the multiple Pokemon which lose access to it, and so cannot use the same sets anymore. By banning "part" of a Pokemon, rather than the Pokemon, you ban part of other Pokemon too, even if they were not a problem, causing collateral, which is bad. On the other hand, you can argue that banning a Pokemon means banning all its sets, even if only one was a problem, causing a different type of collateral. As mentioned earlier though, defining what qualifies as a "set" is a grey area, and often the set which leads to a Pokemon being banned is the best/sole set anyways. The unique/defining aspect of a Pokemon is also often part of why it's banned (rather obviously, when you think about it, as otherwise other Pokemon could run the same set but even better because of their unique aspect). So if you ban the unique part of a Pokemon to "save" it, then you've still lost the most meaningful aspect of it anyways.
A benefit of banning Pokemon as opposed to other elements is avoiding subjectivity in which element should be targeted. The reality is that there can be, and often will be, multiple non-Pokemon elements which "break" a Pokemon, where without all of which, it would no longer be a problem; even if there's usually one that people will jump as if it is completely to blame. This not only introduces a lot of subjectivity into which of the options should be banned, but also into deciding which elements would be "enough" in the first place, or which has the least "impact" when banned if you're factoring that in. This means that on top of the necessary debate over whether a Pokemon is banworthy or not, the unnecessary and quite subjective debate of which specific element should be banned is introduced on top, which is a big negative.
Now obviously, not all Smogon bans are actually Pokemon bans, for better or for worse. Generally speaking, if a non-Pokemon element is to be banned though, that element should be the cause of multiple Pokemon becoming banworthy which would not be otherwise. If there's a signature element on a banworthy Pokemon, and you think should that should be banned instead (e.g. the topical Last Respects on Houndstone), that's a no-no, you cannot ban part of a Pokemon to "save" that Pokemon. You
could get into subjective arguments about how that element would hypothetically be on other Pokemon, but that shouldn't be a basis for tiering. It's also, frankly, unfair to other banned Pokemon, there's moves which otherwise see little to no use which could be banned to "save" those Pokemon but aren't since they're not unique. We don't ban Wicked Blow for Urshifu-S, and we don't ban Leaf Blade for Kartana either. The approach to tiering should stay consistent: ban the problem Pokemon, not part of it.
A Quick History of Some Combinations in Doubles
So, you should stick to banning Pokemon as opposed to other elements, all well and good, but this doesn't provide a clear answer for a more complicated scenario: what if a situation arises where a
combination of Pokemon arises as the problem? Let's go through some examples in doubles:

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Belly Drum Azumarill + Follow Me Jirachi (XY DOU)
Near the end of generation 6, a problematic duo was rampaging across doubles, pairing Belly Drum Azumarill + Follow Me Jirachi. Jirachi, now banned in every generation of doubles including XY, could use its comfortable bulk and potent Steel-typing to safely redirect away any attacks, while Azumarill set up and went to town with Aqua Jet (plus Knock Off or Play Rough). Notably, other redirectors were far less effective: Amoonguss, while good, cannot redirect opposing Amoonguss or Safety Goggles users (a common item in the format due to Amoonguss' prevalence), while other Follow Me users like Togekiss were just much worse redirectors, lacking Jirachi's lethal combination of stats and excellent defensive typing. Jirachi, quite differently from now, was also largely seen as unproblematic outside of the duo in question, at the time. So, this case was viewed as the broken combination of two otherwise fine Pokemon, with it being up for debate which if any of the two should be banned, the enabler or the beneficiary. A controversial banning process followed which I won't get into here, but the resolution of the situation from a modern perspective is, Jirachi
is broken, even without Azumarill, so that is banned, while Azumarill is free and not a problem without it. To summarise: we banned the enabler of the two Pokemon, since that was the problem Pokemon, even though it was not providing or using the boosts.
Why didn't we ban Follow Me instead though? That would have solved the problem, and "saved" Jirachi which 100% would not be a problem without it, and actually a cool Pokemon to have as an option. I'd argue you "lose" less with that than a Jirachi ban, especially since Follow Me is pretty niche otherwise in the tier and Rage Powder still exists as a much fairer form of redirection. Follow Me practically exists to enable strategies like this, and is quite restrictive when on an actually good Pokemon, there's a reason it gets stuck on bad Pokemon and two of the best users in DOU (Jirachi and Blastoise) got it via event so VGC never had to deal with them. Now of course, I don't actually think it should be banned, and banning it at the time was unthinkable since nothing else with Follow Me was an issue. What if that wasn't the case though, what if Follow Me was exclusive to Jirachi? Well then you'd have the same problem combination come up as before, but now some people would want to ban Follow Me instead to "save" Jirachi. If you gave one more Pokemon Follow Me in this hypothetical, one which would also be a broken redirector, then you'd have a lot of people wanting Follow Me banned. Except nothing about Jirachi itself has changed, and yet because of the change in which, if any, other Pokemon gain access to the same move as it, people's position on whether or Jirachi it should be banned has changed. Sticking just to Pokemon bans avoids these complications by being consistent: Jirachi is banworthy in each of those situations, so it should banned, regardless of what other Pokemon do or don't have Follow Me. Hopefully this thought experiment demonstrates why non-Pokemon bans should be avoided.

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Beat Up Whimsicott / Dragapult + Justified Terrakion / Cobalion (SS DOU)
Historically, Beat Up + Justified (targeting your teammate with Beat Up to activate the Justified boost 6 times) is a common ladder gimmick in doubles, something which could catch you out if unprepared, but not a serious threat in tournament level play. Early in generation 8, before Dynamax was banned from the tier, this was not the case, as Dynamaxing the Justified user made it an almost unstoppable threat, making it immune to Fake Out and much more difficult to KO, while also being able to attack and often even KO through Protect. With multiple Beat Up users, and multiple Justified users (though Terrakion was clearly the best one), none of whom would be a problem outside of the combination (neither the Pokemon nor the move), Beat Up is the element which was banned as a result (a ban since reversed after the removal of Dynamax). Now some doubles players might be reading this and thinking "Well actually, only Terrakion was a problem, Cobalion wasn't
that good" in which case I'd argue you're saying that actually only Terrakion was banworthy and so that should have been banned instead of Beat Up. To summarise: we banned part of the multiple enabling Pokemon, which was in part providing the boosts to the multiple Pokemon being enabled.

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Commander Tatsugiri + Dondozo (SV DOU)
Now we reach the main topic at hand, Commander Tatsugiri + Dondozo, a combination of two Pokemon both from the new generation. At the cost of becoming unusable (but semi-invulnerable), Commander Tatsugiri will provide +2 boosts to Dondozo in each of the main 6 stats and immunity to phazing. Sometimes this will be used in such a way that Tatsugiri will die after activating Commander so the player can still make use of that slot; Costar Flamigo has also seen limited use to further take advantage of the boosts. As mentioned in the OP, there has been some debate over which element should be banned, if action were to be taken. Similar to how the AzuRachi situation in XY was perceived to be at the time, there is a combination of two Pokemon which are a problem together, but not individually (though unlike with the prior case, one isn't actually just busted period).
Well clearly the solution is to ban one of them, though since both are individually fine, and both probably not too significant otherwise if you're factoring that in, the choice isn't completely obvious. Some people think it should be Dondozo since that's what gets the boosts, but I disagree, the offending part of the combination comes from Tatsugiri. Tatsugiri uniquely provides +2 boosts to Attack, Defense, Special Attack, Special Defense, and Speed to its partner, Dondozo not uniquely happens to be pretty good with those boosts. If you asked what about Dondozo makes it banworthy, what would the answer be, that its name is "Dondozo" which means
another Pokemon can give it absurd boosts via
their ability? If you asked about Tatsugiri, then you could answer that it gives six +2 boosts to another Pokemon. That Dondozo is the only Pokemon these boosts can be given to is no fault of Dondozo's. If Commander worked on multiple different Pokemon it would be even clearer Tatsugiri was the problem, same with if Commander worked on an existing Pokemon instead. You can point at Commander specifically, but that's an ability on one Pokemon, so the correct approach is banning the Pokemon with that ability, again pointing to the answer being Tatsugiri. If you want to look at historical precedent, then we've already banned the enabler Pokemon of a combination before, so Dondozo doesn't have to be the one which is banned just because it's the one taking advantage of the boosts and therefore the face of the combination to the masses. To be clear, I'm not saying the enabler Pokemon of a combination is
always the one which should be banned, that depends on the exact situation, but it
can be, and in this case it's clearly at the heart of the problem with this combination.
On Ruling DOU-specific Interactions
However, there is a problem with the above premise: it does not actually account for the fact that this tackles a DOU-specific interaction; specifically, it involves a specific-partners-on-the-field dynamic. There is emphasis on
specific here: it is a mechanic that involves a Pokemon with Commander and Dondozo. There is also
emphasis on partners: OU does not have Pokemon being "partners" on the field due to the format being 1v1.
These properties of being
specific and
partners-based are what necessitate us to reconsider how we approach how we tier DCT. The premise of a Tatsugiri ban specifically is based on how we seemingly cannot separate the ability Commander from Tatsugiri... but what if we arguably can? In a singles environment, Pokemon are often working individually with their interactions with their teammates being quite passive in much regards—they are essentially 6 Pokemon acting independently. A doubles environment, however, gives freedom for more active intra-team dynamics and gives way for doubles-exclusive synergies, which Commander specifically mechanically allows in a unique way. The premise of Tatsugiri and Commander being inseperable is a failure to see Commander as it actually is: a specifically promoted synergy between Dondozo and Tatsugiri.
One can still argue that it is Tatsugiri specifically that we should ban because it is its
own ability in Commander which enables the strategy in the first place. However, we must recognize that the burden here does not lie in Tatsugiri itself. We actually
can assert that the viability of Dondozo plays a part of assessing DCT as a strategy as whether or not it itself was up to par would affect the strategy's power, ergo we actually
can assess Commander by itself by virtue of something else interacting with it. To date, there has been no other ability in the game which requires a specifically named
other Pokemon in its description (per my sources

).
To add to this, there is also actually precedent already for a ban based on DOU-specific interaction, and that is early SS DOU's Beat Up ban during the Dynamax era. It similarly involves a specific-partners-on-the-field dynamic that DCT has, this time a dynamic between a Pokemon with Beat Up and between a Pokemon with Justified. Of course, the DCT and the Beat Up ban are mechanically different, particularly in speed of strategy and nature of interaction, but the premise is essentially the same: both involve one Pokemon bolstering the other in a manner only allowable by a doubles format. The Beat Up ban removed the specific enabling element, which is Beat Up, but this also had the property of the move being accessible by a wider pool Pokemon. In DCT, the proposed Commander ban would be still consistent despite the more limited accessibility as it would still hit the same thing: the specific enabling element; to the argument that Tatsugiri should be banned due to availability, refer back to the paragraphs above.
Memoric emphasises that this is an
on-the-field-partners dynamic between
specific Pokemon, but these have no bearing on which element should be targeted. If a combination of two Pokemon are a problem, one of the Pokemon should be banned, that much should be clear by now. What difference does the partners being on-the-field together or not make to that? Yes, singles obviously cannot have on-the-field-partners, but that isn't a reason to deviate in tiering approach. The same reasoning behind sticking to Pokemon bans applies.
Commander
IS inseparable from Tatsugiri. It is the signature ability of Tatsugiri, no other Pokemon naturally has it, and you can't pass it around with the likes of Skill Swap or Trace either. Dondozo does not start with Commander, Dondozo does not gain the ability either, Tatsugiri provides Dondozo boosts with
its ability Commander. Clearly the effectiveness of the combination does depend to some extent on Dondozo's own merit, but that doesn't change the fact that the ability still belongs to Tatsugiri and Tatsugiri alone. Other combinations have also depended on the viability of several Pokemon (naturally, since they're combinations), Jirachi relies heavily on its partner but we still banned that. Commander requiring a
specific partner does not change the fact it is on a single Pokemon, whose own viability also affects the strength of the combination, so by policy it is clear that a Commander ban should not be on the table.
Beat Up being the element targeted in that situation is tangential to it being a doubles-specific interaction. There was a situation with multiple Beat Up users, and multiple Justified users, i.e. multiple Pokemon would have otherwise required a ban, so a non-Pokemon element ban became available. As I said earlier, if you think only Terrakion was banworthy, then that just means it should have been banned instead. Being a doubles-specific interaction does not change how the tiering approach to it in terms of banning a Pokemon or not should be.
PS: I personally
do think Dark Void should be unbanned in SM DOU, but people have complained whenever it's been brought up before so I've never pushed the subject. Same with how GravSleep should be a Gravity ban instead (and doesn't need to exist in SM), and BW should remove the abomination which is Sleep "Clause" Mod and replace it with the move ban it's already been changed to in singles.