>>36138652It's true that some legendary pokémon are not unique, but obviously the Mewtwo that appears in Kanto in HG/SS is still the same as the FR/LG one, so Red didn't catch it in the games.
In addition, whenever the player is going to capture a main legend it is stated that the legendary pokémon is testing the player or that they want to be his friend (Ho-oh, Dialga/Palkia, Zekrom/Reshiram).
It is also pretty obvious that the protagonist of the games is not just a trainer.
