The fact mainstream media touts an scientific paper is irrelevant. The thing that matters is the paper. And that 2017 paper you posted is filled with problems that even the authors themselves recognized.
First look at where in Egypt they got their samples from:
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That's Lower Egypt near the Delta. At the time the study claims these samples were taken the Ancient Egyptians had already moved the capital city down south to Thebes aka Luxor. I told you already in this thread that Lower Egypt had a more mixed population than Upper Egypt thanks to an influx in foreigners after the rise of Ancient Egypt into a superpower. The authors themselves admitted that if they took samples from Upper Egypt (where the Pharoahs and origins of Ancient Egyptian civilization lay) the results could have been different. I don't know how many times I have to repeat myself but the Pharoahs came from Upper Egypt. You see that city at the bottom called Luxor. In ancient times it was named Thebes and it was the capital of Ancient Egypt for the Middle and New Kingdom. See here:
Thebes, Egypt - Wikipedia
You cited a study conducted by dishonest scholars. And this is why I caution against simply reading a headline from a DNA article and taking it as gospel. These scholars picked mummies from regions that everyone knows included non-native Egyptians at the time in question and then claim these DNA results as being representative of Ancient Egypt as a whole and more importantly totally ignore the fact the ruling class didn't come from that region in the north but rather came from the south.
The DNA article I cited that was published just 4 years earlier in 2013 found different results because it studied mummies from the royalty that lived in Upper Egypt (an area more to the south free of foreign influence from the Middle East). These mummies showed the closest genetic affinity to Sub-Saharan Africans from the Great Lakes Region.