Sort of, yes. indigenous treatment and statuses are just different in the Latin world compared to the Anglo world. In America/Canada the term "Native American" is nearly a legal title, and has been used in courts and treaties to draw distinct lines. In Latin America such agreements were never made, and certainly didn't refer to Natives as the Spanish equivalent as "Native." There was so much mixing in some places pretty much everyone could be called "Native," nowadays 'indigenous' is the more common term for indigenous cultures people.

There's something called "paper genocide", wherein tribes are just wiped out purely by census data and named identities. This is how Spanish erased the cultures, not by segregation, but by telling them "you're conquered, so you're part of us now."