Should I stop thinking about the logic of the Pokémon universe or be concerned that at least 70 new species of Pokémon get added every few years? I mean, they’re all coming from somewhere
But a lot of the Pokémon from previous generations can still be caught in the new games (in Sun and Moon, about half of all Pokémon are in the Alolan dex). In Fire Red, I think about 170 could be caught, which means that it updated from the original. The fact that there’s over 800 of these things and they all seem to be hopping into different regions in the 22 year span in which these games were made makes me think there should be some Australian rabbit problems with the entire known Pokémon world.
Hence “native” species.
I think any Pokémon coming in from the old games are brought there from their respective regions.
As for why it doesn’t happen in reverse.. Well, that’s just because Gamefreak doesn’t have any Sapphires.
Er, that is to say, they can’t see the future.