Egypt is both Mediterranean and African though, and Egypt had long been influenced by other cultures, commuities, and networks and trades long before the Ptolemies. These communities never existed in vacuums. And while yes, Cleopatra's family was Greek/Macedonian in origin, you have to also consider the scope of the time. We're talking three hundred of year between Alexander becoming pharaoh and Cleopatra dying. At this point the family was also Egyptian. Even though Europeans forcefully took control of the Americas we wouldn't say that Tom Englishman who's family came to the Americas 300 years ago is English, not American.

And as Bentresh has already pointed out, you cannot judge by the appearances in the art as to whether those people had Greek origins or not. These things, as is often the case, are more complicated than they appear.

Your understanding of culture is so shallow it’s frustrating. Culture is this constantly evolving thing. Cultures mix and transform and create something new.

Part of the reason why the Ptolemies kept a hold of Egypt for the best part of 300 years is their willingness to adopt the traditions of their new homeland. By the time Cleopatra VII was Queen no one (including Rome and her own subjects) saw her as anything but an Egyptian Queen. As for the local Egyptians, the vast majority seem to have been on board these changes and many adopted Greek customs themselves.

Modern DNA analysis suggests that Fayyoum (where these new mummies were found) is actually very homogeneously Egyptian, indicating that throughout its history it was relatively immune to waves of migration.

Whether you like it or not, “ancient Egypt” has been dramatically influenced by waves of its early invaders. These include the Greeks and Romans, but also the Nubian kingdoms in ~1000 BC. The Hittites and the Hixos. The Persians from the east and the Libyans from the west. That’s just how these things work.

As others have said, Egypt is culturally African, Mediterranean, and Arab.

How long does a group have to live somewhere to be indigenous?

Well if you think that native Americans are an indigenous culture to North America then that would be incorrect because they descended from ancient paleo Siberian’s ( in fact some DNA evidence suggests they may also have been European... https://www.science.org/content/article/scienceshot-native-americans-were-mix-asian-and-european ) so they aren’t indigenous either according to your metric. You see how silly your hypothesis is?

As someone said, your understanding of culture isn’t very well developed or cogent. Just stop with the silly indigenous stuff, cultural osmosis is a thing and there is no ‘definitive’ culture in any given area on earth. It’s all a constant adaptation to and amalgamation of various cultures intermingling over time. A future civilization discovering a US president and describing it as an ancient American would be entirely true relative to the time period from when they discover it.