In order for "native" to exist, there must be a "non-native." If I'm talking to an international student from Germany at my American school, I'm the native. If I'm talking to someone who grew up near my school, while I come from several states away, they're the native. That's the explicit definition.

I come across the situation you mention all the time. I study cultures of early north-central Peru. I meet a lot of non-history/antrhopology people try to be super "aware" and fight the system by talking about those bloodthirsty Spaniards who trampled into the Inca cities with their horses, slaying all who stood in their way of the piles of gold stored in unguarded temples as the naive, good-hearted Inca threw their wooden sticks that bounced off steel armor. (How demeaning that is to the Inca is another story.) Naturally, I tend to view the past through the people I know the best. So for me, the Inca are those weird sun-worshipers from the south, barging up north and absorbing everything they can, whether through diplomacy, warfare, or trade. Fifty years later the Spaniards came in- they're just another big empire looking for more land and resources. The two are just as "non-native."

An interesting modern perspective on this affair can be found in Catherine Allen's classic ethnography The Hold Life Has. It discusses life in a modern (late 20th century) village that strongly identifies as "indino" or "Runa," the best Spanish and Quechua equivalents for what we would call indigenous. It addresses several interesting topics related to indigeneity: the necessity of a solid Runa (native) - Misti (mestizo) divide for the existence of both categories, the diminishing "purity" of Runa life and its adaptations to city culture, and the creation of Runa culture from Inca roots, colonial practices, and modern revivalists.