Well, according to your definition Penelope Cruz and Cristiano Ronaldo are native to Portugal. Their genome, as you put it, "...dominantly reflects the (genetic) substratum of his region ..." Even if Ronaldo great grandma was (possibly) black, he is dominantly 87.5% autosomaly Portuguese, therefore native. Isn't 87.5% dominant enough for you? What's your percentage?
Penelope is at least 75% Portuguese, 25% Gypsy. Oh wait, Gypsy live in Portugal for 600 years. How come they are not included in Portugal autosomal substratum? 600 years is not long enough? Where is your cut off for native, one thousand years?
See, whatever definition for "native" you will find, it will look only good on paper, but it will become vague and imprecise when thrown against complexity of today's societies.
PS. I'm pretty sure we wouldn't have this conversation if Penelope and Cristiano were blond, right?