>>34357093If the past few games have taught us anything, it's that Pokemon is taking a Rick & Morty approach to its timeline. Everything is canon in each version, it just all happens in different universes. Which is the "correct" version is impossible to say and it doesn't even really matter.
Considering nothing else from Yellow has ever carried over, I don't know why the Pokemon he uses is indication of anything anyway. They simply gave him the best known/most commonly used Pokemon, since he was supposed to be the player after all.