Two things.

First,
I'd like to nip in the bud that theory of the 12 not existing. They aren't just a cage for Bahamut.
Case in point: prayers during the invasions gave buffs and debuffs based on who you prayed for.

Second,
I agree with this idea that perhaps atomos might work for bahamut.
Why? The invasions. They had deepvoid enemies. Minions of Atomos.

Perhaps he was redirecting the aether from the aetherytes towards bahamut in order to empower him.

Not 100% sure, just think its a viable explanation for Atomos and the deepvoid monsters throughout the invasions.