Hmm, I still don't know if I believe in this theory (of him being a Ganon/Gerudo ancestor) or not, but the skin colour issue can be resolved easily. We know that the Gerudos live in the desert afterwards and therefore the skin might actually become darker over several generations by the means of evolution.
AFAIK this is also the most accepted reason why human skin colour differs in the real world with latitude. In areas with high sunlight exposure, darker skin protects against too much UV radiation; where there is less sunshine, a rather light skin lets through more UV which is necessary to photochemically produce Vitamin D.
This evolution took hundreds of thousands of years in the real world, but we all know that Hyrule is a magical fanatsy world so it might have gone faster.