Ahem.
Tho as you yourself said, this isn’t the reason, but it is a reason.
The more I think about it the less I agree with the idea as being a "big" reason. Certainly there's a number of Pokemon that were getting overhauled to the end, but...
Falkner, for example. Hoothoot was locked down for literal years, and even by 97 Noctowl was something on deck. The details were being ironed out, but the concept was still pretty firm. But Falkner uses neither of them despite this; hoothoot in particular would have been EXTREMELY easy to sub in for Pidgey even if they felt Noctowl (which still wound up on a few teams iirc) was a no-go.
Pineco was a very late in the game decision so it, and Forretress, being out because of that makes sense...but Ledyba & Spinarak who despite some tweaks still being made were basically throw away fodder that could have easily been on Bugsy team instead of 2 cocoons. Not like they're very strong Pokemon either so the conceit of "the REAL boss is Scyther!" would still hold.
Heracross also seemed to be around for a while and fairly ironed out, but didn't land on either Chuck or Bruno's (who did at least get Hitmontop) team.
Slowking was one of the OGs of Gen 2 and still got the boot for a second Xatu on Will's team.
Meanwhile
Sneasel was a Pokemon that had been through the wringer in terms of design basically right up to release but still landed on Silver's team through a large chunk of the game. Piloswine didn't exist at all until later on and almost had an evolution at one point, but still managed to be Pryce's ace*. Fortress was a very late addition that had to go through a couple design overhauls but still landed on Koga's team as one of the penultimate bosses of the first part of the game.
*Honestly typing all this out, I think we as a community might slightly overexaggerate this issue with the Leaders particularly. 4 of them still have gen 2 aces and a 5th has a Pokemon that at least
evolves into one. All the E4 have gen 2 members and 3 of them have them as their ace. And heck the Kanto leaders also have 5 of them with gen 2 Pokemon. Like they definitely could have used more (lord knows there's plenty of normal types Whitney could have used & Bugsy just did not need to be using 2 cocoons c'mon now) and the randos around the world should have used more, but the way we talk about it you'd think everyone was Morty. Really the gen 2 leaders just have other issues like number of Pokemon (why Chuck have 2 pokemon??) or poor decisions on double ups for their placements (why Pryce have dewgong AND seal? why didnt Jasmine at least evolve the other Magnemite? Why bugsy) or level (but that's All of GSC so...)