Yes I can remember there was a lot of anger when the archaeological evidence was released by the Yale-Cambridge group on the strong possibility that North-of-the-Sahara pre-Roman Empire ethnic groups were more Aryan than they were African. There was a strong early eighties movement that insisted Cleopatra was black that was based on the idea to point out that Africa was a rich and strong and vibrant set of cultures and societies long before "white" colonization.I think that it the fuss is caused by the fact that it would suit certain cultural agendas to identify various famous historical figures as either black or white- probably not a very PC comment to make, but there you are!
While the later is certainly irrefutable many of the proponents do not like separating Northern Africa from the rest of the continent as they see it diminishing the continent's accomplishments as a whole.
History and archaeology though tend to see Egypt and what was seen as a Gaetulian section of Africa as ethnically separate for some time and later melding much more with the various Asian groups as they expanded and immigrated. One of the best lectures I was privileged to attend at the Cairo Museum on the Hyksos and the Nubian "foreign" dynasties made what I thought was the most apt comparisons. Namely that Egypt and the Numidian regions were more like India in many regards. Isolated by geography they were ethnically a rather distinct peoples in a region (The Mediterreanan) that was very same-same. Which is why culturally there was sometimes seen as a greater remove between say Romans and Carthaginians, or Greeks or PErsians than an ethnic one. Appearance wise there was not a huge difference in skin tone. Records on the Nubians, particularly in how the Egyptians defined and viewed them though strongly suggest that they and the Greeks and later the Romans all did have strong skin tone prejudices. Going by both nineteenth and later twenty fifth dynasty records on, Egyptians clearly saw themselves more in line with the ethnic likes of the Hittities and the Babylonians and Assyrians than they did their sub-Saharan neighbors.
And looking at the reactions Romans and Greeks had towards the northern invasions, it seems equally clear that East versus West was actualy much more politics while North and South were more ethnic. Which is hardly what gets played out here. The Macedonians disdain for Persians seemed more favored status oriented and custom oriented than racial bigotry. Much more wariness and racial fears seem to arise whenever the Illyrians came storming down into the Greek Penisula and the Romans were even worse about the Cimbrii and such.
The lack of any real diatribes beyond Cleopatra not being Roman seems to indicate that her ancestry was identifable as being Greek or Aramaic in origin. We don't know who her mother was or who Auletes' mother was in terms of ethnicity but Cicero and the same patrician class that still viewed Latins as inferior certainly did. I strongly suspect that Cato would have had plenty to say if Cleopatra had black ancestry (in fact as her father is the most damning of her ancestors in her contemporary enemies' eyes, it seems that the rest of her provenance was not only known but also relatively respectable to staid Roman bigots). Simply because the purists of the time did draw distinctions at a time when marrying a Latin state native was allowed but a hurdle and even marrying a Greek was basically surrendering one's birthright. Marrying someone from Asia Minor or any the Eastern states was seen much the same as the Victorian English would have someone going "native". Heck just moving to Athens or to Bithynia was either a huge punishment or a huge social gaffe.