Nubians did conquer Egypt,  at some point in history, not sure on the details. So that is their reasoning for depicting Egyptians as black and making a big deal of "kangs" and shit. 

Funny enough Nubians are seen as enemies in ancient paintings so I doubt anyone back then would have considered a Nubian to be Egyptian or allow them to live among them as anything but slaves. I would not mind to know how much of an impact did the Nubian occupation had on Egypt. I would search for an answer but I doubt I can find a good non-biased account of it.