Not at all. Look at Dark Angels, their Veteran First Company, Deathwing, is basically mirrored with bone white armor instead of cloaks and green cloaks instead of armor. Then their Second Company, Ravenwing, is entirely black and white with the bone white cloaks. Absolutely nothing wrong with using cloak color to designate Companies or Roles, Black Templars use the entire shoulderpad to designate roles instead of company. They don't even use the standard markings, just different color emblem, trim, and/or main shoulderpad.