Well
Reviver while the points you do make are true there are also still some pretty big reasons to run Modest.
Modest Choice Scarf Water Spout for example bears the power to OHKO 252 HP Arceus hit neutrally by Water Spout a good portion of the time after Arceus has taken Stealth Rock damage:
252+ SpA Kyogre Water Spout (150 BP) vs. 252 HP / 4 SpD Arceus in Rain: 382-451 (86 - 101.5%) -- 87.5% chance to OHKO after Stealth Rock
Compared to Timid which OHKOes far less frequently:
252 SpA Kyogre Water Spout (150 BP) vs. 252 HP / 4 SpD Arceus in Rain: 348-411 (78.3 - 92.5%) -- 37.5% chance to OHKO after Stealth Rock
There's also the issue against 252 HP Water Arceus. Water Spout after Stealth Rock actually has rather high chance to 2HKO if Modest then compared to Timid:
252+ SpA Kyogre Water Spout (150 BP) vs. 252 HP / 0 SpD Arceus-Water in Rain: 191-225 (43 - 50.6%) -- 96.9% chance to 2HKO after Stealth Rock
252 SpA Kyogre Water Spout (150 BP) vs. 252 HP / 0 SpD Arceus-Water in Rain: 175-207 (39.4 - 46.6%) -- 30.5% chance to 2HKO after Stealth Rock
Other relevant calculations:
252 SpA Kyogre Water Spout (150 BP) vs. 200 HP / 0 SpD Xerneas in Rain: 415-490 (93.6 - 110.6%) -- 62.5% chance to OHKO
252+ SpA Kyogre Water Spout (150 BP) vs. 200 HP / 0 SpD Xerneas in Rain: 456-537 (102.9 - 121.2%) -- guaranteed OHKO
252 SpA Kyogre Thunder vs. 0 HP / 0 SpD Yveltal: 272-320 (69.2 - 81.4%) -- 50% chance to OHKO after Stealth Rock
252+ SpA Kyogre Thunder vs. 0 HP / 0 SpD Yveltal: 298-352 (75.8 - 89.5%) -- guaranteed OHKO after Stealth Rock
252 SpA Kyogre Surf vs. 252 HP / 4 SpD Arceus in Rain: 210-247 (47.2 - 55.6%) -- 76.2% chance to 2HKO
252+ SpA Kyogre Surf vs. 252 HP / 4 SpD Arceus in Rain: 229-271 (51.5 - 61%) -- guaranteed 2HKO
There's probably more but yeah its a tad bit hard to find all of them.
There's no doubt Timid's speed boost is very very useful, but I wouldn't call it completely superior to Modest. Modest still has some merit. Erm that and:
Also outspeeds Blaziken at +1 speed which is incredibly relevant.
While this is true, Mega Blaziken at +1 always outspeed, which I do think is more notable then regular Blaziken. Also Kyogre is a terrible Blaziken check in general. If it runs Protect it can use it to nab a second speed boost which pretty much renders the Timid boost in that case somewhat useless.
I will agree that it is nice for speed tying at worse with other things that have a base 90 speed and beating Deoxys-A though.