I would say it's a combination of both with many races. In many cases the humanoid races did evolve from primates, and in some cases created their Gods through the power of belief. But the Gods themselves have been guiding the evolution and development of races. But it varies on many worlds.
Indeed. I should have been a little broader in my first statement. Let me amend it to say: if magic is involved in the creation or development of a species, any variation can be explained as magical in origin.
That doesn't mean humans can't naturally evolve pigmentation we don't normally see on Earth, at least given my layman's understanding of genetics and evolution. I don't actually know all the factors that drove humans to their modern pigmentations, so it's more a matter of me blindly accepting there is a reason in the real world, and then assuming that reason, whatever it is, also applies to my homebrew setting.
That said, it's more a matter of comfort with that model than a scientific argument for or against other variants in pigmentation.