The idea that the Egyptians were Europeans is not a common misconception. Most people assume they're brown like they were depicted in their artwork.

If you actually look at modern genetic studies, the general consensus is that there is a very high level of genetic continuity between the pre-Islamic population of Egypt and modern Egyptian Arabs. I.e you can look at modern Egyptians and get a pretty good idea of what Ancient Egyptians looked like. They are not black Africans nor are they particularity closely related to black Africans (excluding people who live in the far south, who are basically Sudanese).

I don't understand your point about Nubians. Yes, Egypt was ruled by black Africans for certain periods of their history. But the elites hardly say anything about the actual common people. For example, Russians were ruled by Turko-Mongol peoples for many centuries but there actual influence on the Russian gene pool is negligible. For that matter, Ancient Egyptians were ruled by Greeks and Romans for many centuries; are they therefore white? Of course not.