Well preserved mummies from thousands of years ago don't look much different than most Northern Africans today. Of course, the aristocracy wasn't always composed of natives in Egyptian history. DNA studies show a preponderance of haplogroups common to the Arabian peninsula, North Africa, Caucasus, and East Africa.
Those features that you think are North African can also be found in Sub-Saharan Africa as that is where these features originate. The issue at hand is their skin color, which is a byproduct of their African origin.