I'm sceptical about Atomos being an overtly antagonistic force; at worst, his presence is like an opportunistic infection taking advantage of a plane of existence whose crystals have been weakened with a concomitant lapse in the structure of its local reality. Eorzea's had a fairly cosy relationship with the Void for a while now, viz. the snurbles and their less photogenic brethen tromping all about the place.

Sadly, we probably won't know what the deal is with Bahamut -or- Atomos lore-wise until 2.0 releases. Hopefully there'll be a handy NPC nearby to explain what we missed in the five years we were somewhere south of accepted reality (assuming that we did indeed get sent elsewhere and elsewhen by Louisoix's ultimate sacrifice.) Doesn't mean it's not fun to speculate, though!