Alexandria was considered "next to Egypt." It was the Greek colony from which the Ptolemies ruled Egypt. The Ptolemies inbred to keep their Greek blood and wouldn't even speak Egyptian. Cleopatra was, however, the exception to this, as she learned Coptic and presented herself as an Egyptian Pharaoh.
Sorry, I don't actually think Firaxis is being racist. I was being hyperbolic. Seeing 5000+ of Ancient Egyptian history being represented by its last ruler, who was from a line of colonial conquerors, really grinds my gears. Even if she herself tried to assimilate herself to the culture unlike her ancestors.