You know, this is such a stupid question for several reasons.
The fact that you THINK there needs to be an explanation for dark-skinned Viltrumites in a fictional story is just brain-dead retard activity.
However, if you desperately need an explanation, then look towards the human race as an example. The first humans (homo sapiens) to walk the Earth were ALL very dark-skinned.
That was the default of humanity for a VERY LONG TIME.
So if you employ that logic, you could make a theory that the first Viltrumites to walk Viltrum were dark-skinned too, as you don't naturally gain or increase melanin, you can only lose it.
My point is, you gotta start with a high level of melanin as a species to end up producing other beings with a low level of melanin if the conditions are right. The reverse is harder to do.
Again, asking why the concept of black Viltumites exists is dumb, but this is the best explanation I can give you. It's fiction, though, so just enjoy the show.
I never truly understood the concept of black Viltrumites. How did they get the colour and the hair?