I mean, the skin colors in this game already vary from artist to artist and gameplay to art. Compare Cu Alter's in-game sprite and his command card sprite with his art. Heck, some characters are actually *darker* in secondary sources, there's a lot of CEs where Nitocris is way darker than she in in her card art.

Japan just isn't really concerned with skin tone as representation, so it's something that's going to vary a lot because they see it the same way as, say, hair color, or height, which also vary a lot from artist to artist. I wouldn't attribute any malice to the variation. Not that I'm saying you aren't allowed to dislike it or be made uncomfortable by it.