At least one dynasty was from south of the Sahara. And there is always some admixture- miscegnation if you will- between ruling and slave populations. There is also what seems to be a sociobiological rule that the ruling class is lighter skinned than the subject population in every society with occasional anomalies i.e. the Ethiopian 25th dynasty that ruled Egypt.
You restate the obvious, but you don’t counter the main fact. The Egyptian Pharoahs shared more DNA with the rest of the Eastern Mediterranean rim than they did with sub-Saharan Africa. Much more.