according to Wowhead, blizz may have decided that there will be different colored s13 depending on your faction. apparently, most sets have 3 colors, one of them tagged as "horde" in the game files, one of them tagged as "alliance", and a third one. (I say "apparently" because I haven't seen the game files myself, though I kind of trust Wowhead)
the third one is probably the normal conquest set (with lower ilvl), while the elite conquest sets will have different colors depending on your faction to show your dedication to your faction in the war, similarly to how the war steed and war wolf are given to very dedicated PvP players, depending on their faction.
Taking the warlock set for example:
the purple set is the neutral lower level one which anyone can get.
the red set with black details is the elite set for the horde, while the blue set with dirty gold details is the elite set for the alliance.
now, looking at the monk sets:
the blue and green set is the neutral lower level one which anyone can get.
the red and green set is the elite set for the horde, while the blue and yellow set is the elite set for the alliance.
so, what do you think? is this a good idea, or a bad idea? should it have been extended to the normal conquest gear or should it be for elites only?
personally I'm fine with it, since I wanted the purple warlock set anyways
(but I feel sorry for alliance locks who wanted the red one lol)