Actually the Egyptians never called anyone Nubian. That term was not used in ancient Egypt.
The Egyptian world view focused on the Nile. Whether or not they portrayed other people as polka dot or crossed hatch, they viewed the Nile as Sacred and the origin of the Nile as the origin of the black silt and black clay and black man of inner Africa. Therefore, it was their connection to the black earth and the black mound of creation. It was also the home of black people.

Likewise, they painted both themselves and other Southern Africans both black and brown in various contexts. Anyone that knows anything about the Nile Valley or Africa in general, knows that there are some Africans, like those in parts of Sudan and elsewhere who are jet black. However, there are also many other Africans in the same regions who are medium to dark brown and not jet black. Such variation is natural among Africans.