In FFXI Atomos resided in Walk of Echos as he can't completely exist in bodily form himself, much like Alexander. The Cavernous Maws you seen were basically his Avatars much like the one Cait Sith summons is the avatar of Atomos, so these could literally be 'Avatars' of Atomos itself or it could be that many entities make up "Atomos."

I haven't seen the quest yet though.