The Chagossians aren't a counter-example to that at all - they were moved to the islands by European colonialists as a slave labour force, which as I understand it were uninhabited before.
What, did you expect a new lineage of humans to evolve separately there or something?
Of course "native" can be arbitrarily limited to mean 1000s or 10,000s of years, but even after slavery those people lived there for at least five or six generations. So from the perspective of the people being forcibly removed, getting their pet dogs gassed by the military, it really wouldn't fucking matter.
And the Wikipedia article says they're "native", which you explicitly claimed was not the case.
This is completely wrong. BIOT includes these islands where the native people were forcibly removed and the story is terrible.
https://en.wikipedia.org/wiki/Chagossians
https://en.wikipedia.org/wiki/Expulsion_of_the_Chagossians
It's not like this hasn't been discussed many times on HN before. I own a .io but come on!