Where? The only PZ I can find for her is the final rematch in BDSP, which yes is odd, but...
So her team is basically set as: Spiritomb, Lucario, Milotic, Garchomp (all of which are reasonable "boss" mons for various reasons). Then the remaining 2 slots have always* been some mix of Roserade, Gastrodon, Togekiss, Glaceon. Which are all perfectly serviceable, but not as impressive. First off, why any of those, but also, once established, why change them? Given that, swapping one of the two floating slots for PZ isn't a huge departure, and it's certainly more intimidating than Glaceon or Roserade as her special attacker.
*BW gave her an Eelektross and a Braviary for some reason, but it seems like the devs wisely decided to move on.
So, to answer "why any of those":
-Spiritomb is kind of a given for her as an archeologist: the Odd Keystone is the sort of thing she'd have found at a dig or in an old ruin somewhere
We know that she also undertook a Pokemon journey like the player did, so her having a variety of Pokemon from all over the place makes sense, but her Pokemon tend to be elite-tier rare ones with very few weaknesses. Milotic is a fantastically rare species only used by bosses and Ace Trainers, Lucario is an egg-exclusive species, Togekiss is another rare egg-exclusive species (and is justified by her giving the player a Togepi egg in Platinum). And then there's Garchomp, of course.
Gastrodon fits her the least, which is why I suspect it was replaced in Platinum, but it's broadly in keeping with the others as a Pokemon with only one major weakness. Eelektross continues that theme so I can see why it was given to her in BW - Braviary less so, but it's one of the strongest bird Pokemon so may have purely been for aesthetic variety (and also to showcase a mon no other major NPC in BW uses - Alder should have had it from the start imo, fits him so well). Her getting a Glaceon again adds some good variety and better Sinnoh rep - it's again a quite rare species.
I never actually finished BDSP so until now didn’t bother checking what mon Pory-Z replaced on Cynthia’s team. I did know she used one but I’m pleasantly surprised to see that they replaced the mon I also would’ve chosen to replace.
I don’t think there’s any more consideration required for Cynthia’s team besides “rarity”. For that reason Roserade always felt extremely out of place to me, Budew is everywhere at the start of the game and Roselia is fairly common in the mid game. I always thought that they just gave it to her because first female champion and they have this cool new female-looking Pokémon, with no greater underlying thought put into it, and I always found it tacky. It doesn’t help that Roserade was the ace of the SECOND gym leader, and sure that’s a pretty tough fight but seeing a mon used by the second boss of the game come back as this champion-level party member was always weird.
Gastrodon is similar, but Diamond/Pearl were playing with scraps and the “well this colour is only half of them!” was prob adequate for their scarcity bar at the time. With more options they quickly replaced it.
Across all Sinnoh games Cynthia’s party members, from the player’s perspective, are 4 gift mons (Lucario, Togekiss, Porygon-Z, Glaceon), Spiritomb which is a one-off you have to muck around in the underground to get, Milotic which involves catching a Feebas and we all know how that works, Garchomp who’s only in the hidden entrance of an optional cave, and then 2 generic common mons in Roserade and Gastrodon. Where every other category falls under the umbrella of rare or scarce, Roserade and Gastrodon have always been the members who feel out of place.
Porygon-Z is a great addition since it’s always only ever been a giftmon or arcade reward. I’d go so far as to say it probably would have replaced Roserade in Platinum too but at the time it type overlapped with Togekiss, and now that they had the expanded dex they probably would’ve thought it a bit underwhelming for the champion to double up on Normal-Type of all things.
To expand on the Roserade point: while Roselia is immensely common in Sinnoh and elsewhere, Roserade is seen vastly less, implying that evolving it takes more time, effort, or skill than your average trainer possesses. It's similar to the way in which, for instance, numerous trainers in Blackthorn Gym have a Seadra but only Clair appears to have managed to evolve hers into a Kingdra - the implication, to me at least, is that Roserade is not a particularly common or easy Pokemon to obtain. Yes to we the player it's as simple as applying an evolution stone but that's a gameplay mechanics decision; and Shiny Stones are only buyable in a couple of games so they're very plausibly extremely uncommon in-universe.
I assume Porygon-Z feeling out of place on Cynthia's team is more a function of what kind of Pokémon it is, rather than what it provides to her team. She's a researcher/archaeologist, and a lot of her Pokémon, outside of their strength, represent some sort of natural power or overworld rarity. Spiritomb, Lucario, Milotic, Togekiss, and Garchomp are all rare, with Spiritomb and possibly Chomp linking into her archaeology habits, and Lucario and Togekiss into her passion and personality.
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Meanwhile, Porygon-Z is anything but natural (it's even a digression from Porygon's intended programming), and it doesn't feel like it fits her interests outside of battling. I could definitely believe that ILCA gave her Porygon-Z to make sure it was represented by one major boss trainer in the game without really thinking about it on her team.
Yeah, this is what I was getting at. Porygon-Z isn't the
worst imaginable choice for her from a gameplay point of view, it just stands out quite weirdly against her other picks because it feels incongruous from a character standpoint. There's a slight undertone of high fantasy to Cynthia's team picks: an ancient ghost, a dragon, a noble warrior, a legendary sea serpent, an angelic bird, a tricky grass fairy*. Whereas Porygon-Z is futuristic, inorganic, not particularly noble or dignified.
*not a literal fairy of course, but Roserade certainly has some magical vibes going on