If this was a complete reboot them a white Khan would be fine, however it is not.
So time travelling Romulans turned a three hundred year old Indian into a Northern European?
Sure, the same way they turned Jim Kirk's eyes blue at the moment of his birth and caused everyone else in the universe to look different as well.
Khan looking different is absolutely fine for the same reason everyone else looking different is.
It's all the way it is, not the way some folks would have it be, and it's fine.