> the seemingly strong conclusion that Ancient Egyptians did in fact move to Egypt from Mesopotamian
Touch some grass, seriously. They looked at the DNA of 1 (in words: one) guy and now it's "hey in fact Egyptians all came from Mesopotamia"? You'd have to take many more samples to support such a broad claim, and it's not because of the Ministry of Antiquities suppressing ideas.
Mankind likely did not originate in the Nile valley, hence the fact we find people there from some point in history means they migrated from somewhere else. If you subscribe to the single-origin story (which I think is plausible but not the only possible one, the alternative being various human populations that got separated and re-united in different parts of the world) and think, just for the sake of argument, of Lucy as 'the first human' then humans are immigrants almost everywhere (this will be hard to swallow for lots of people and we know from the historical record (https://www.youtube.com/watch?v=eIJF2RomfGE) that the Voth had problems with that, too, so it's very human).
The narrower Nile valley must have been a relatively inhospitable place for a human during the African Wet Period. When that came to an end around ~7ky ago or so that change made the Nile valley rather suddenly more attractive to many thousands of people who used to roam the lands to the right and left of it. As desertification progressed, communities were forced to go someplace else with some ending up in the Nile valley. In a way, you can to this day see the echoes of that time in the ethnic and cultural diversity of Egyptian society which I think is more of a hallmark of this civilization than an imagined homogenized one-mold-fits-all view.
And it's totally not out of place that some people with roots in Ancient Egypt should have an ancestry that came from the Levant or further from Anatolia or Mesopotamia. Egypt was a big place, rich in people, culture, food, arts and opportunity (and, not to forget, regular festivals with beer, wine and music at the cultural centers; today people cross continents for taking part in festivals with beer, wine and music). Egypt had trade, diplomatic relations and 'military exchanges' (war) with those far-flung places and captives were either maimed or indentured, so as a matter of course we find Egyptians with Mesopotamian admixtures, what did you think?