I read an article the other day, if I can find it I'll post a link.
The article stated that the different types had different levels of aggressiveness. Supposedly the maroon is the most aggressive of the bunch. The false perc being the least aggressive. Certain ones may also grow slightly larger than others. If you are trying to get a clown to pair up with an anemone, they have differing preferences.
I think it also said not to keep a false perc and a true perc in the same tank. But you could potentially keep two different colored true percs. If the tank is large enough.