They're not native to any region, the starters from X/Y show us this. Where exactly? Idk. They're meant to be rare so new trainers don't release or replace they're first pokes.
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Why the X/Y starters? They all have to come from somewhere! I've guessed the professors must have gone to Pokémon university to get some kind of degree so I think they are native to whatever region the university is in!! Maybe part of the deal is you can catch 3 of these rare Pokémon & take them home with you!