Although Northern Egypt at that time was more of a cultural "melting pot" at that time than it is today, Moses' parents and ancestors (according to the Bible) were Semitic people of Middle Eastern origin. So, no, it makes no sense that he is depicted as a European. There is scant evidence that Moses even existed or that the Hebrew exodus even occurred. So I try not to get too bothered by any details. One odd point worth making though is that the ruling class pharaohs ruling Egypt at the time were actually not native Egyptians but were foreigners from Europe who had eased their way in. Even the mummy of Ramses has red hair. So, as usual, Hollywood has got it backwards by making the pharaohs dark-toned and Moses light-toned.
But to answer your question, given the last 500 years of western history, the main reason for the discrepancy must be racism. It's the same reason that in history we discuss at length the Macedonian conquest of Egypt, but no one ever mentions the Kushite conquest of Northern Egypt and the subsequent 25th Dynasty of Nubian Pharaohs. In fact, the Nubian Kingdom to the south of Egypt (where the people had darker skin) was just as impressive as that of Egypt and yet is completely ignored by the historical canon taught in schools.