Basically
Emiya, like a lot of characters, has an "Alter" version, which is usually the edgy, evil version. From a lore standpoint, Emiya's tanned because using his magic basically frys him, making his skin progressively more and more tanned, and Emiya Alter is basically when he takes that to the EXTREME where it basically burns him to a crisp.
Still with me?
Tl;dr, the person who was in charge of designing Emiya Alter for FGO designed him under the mindset of "What if Emiya went to prison", and the game isn't subtle about it either. When he's introduced, one character remakes he acts like a drug dealer, and in the Japanese version, there was a joke calling him "Detroit Emiya", or Demiya. Said joke never made it to the English version, and his skin color was changed in the English version to be less stereotype-ish.