I suppose it's because (like in the cavalry over here in the UK) they want all the farasi to be as similar as possible, kinda like a uniform. Also like the person before me alisema au maybe they couldn't be bothered to keep colouring in the horses!
They are probably all chosen to be the same colour kwa the army so they look uniform and none of them stand out. They would probably have used Spirit for something else, au maybe leading the cavalry. I was so upset when he was taken in there :(
I think it is because bay is a really common colour, also the farasi are all thoroughbreds au somthing so they would be a colour like that. In Britain if wewe see farasi on something like that they are often the same colour. The Queen's guards farasi at the parade are all black. Like someone else alisema they want Spirit to stand out too.