Well, several characters in the movie have not the exact same color as their pony counterparts. I think it woud just be a huge step into uncanny valley, if they were the same because of the human bodies. They tried to give them an overall decent design and color is an important part of that.
~StatesTheOblivious~'s post in Why does Flash Sentries human and pony color's not match like everyone else? was marked as the answer