Units developed early on in EB1 tended to have a similar color, but I can recall a couple times the Epeiros people asking for green to be changed to something else in a newer Epeiros unit.

I think it was just habit for the early skinners. If you are making units for five different factions, and you can only have one skin per faction, you want them to all look different from eachother. The easiest way of doing this is with base colors. How do you choose who gets what color? The faction's color on the minimap...