So, first things first let me get this out of the way. Yes, the X/Y legendary auras CAN in fact stack on top of each other, making for insane damage boosts (found in the article here). What I am now wondering is, do reversed auras also stack?
The reason that I am asking this is because, while on showdown about 30 minutes ago I got a Xerneas in randoms. my opponent brought out his alakazam and Mega-evolved it, giving it trace and thus, fairy aura. even with a geomancy boost I didn't expect a moonblast to kill from full, however, it did. that lead me to wonder if it could stack, and after the battle I looked it up and found the aforementioned page. this lead me to wonder, how does this effect work with Aura Break? and thus we are here.
moral of the story, don't send out a trace mon against a xerneas unless it has a stab fairy move.