Two things bugging me with the ending...

[Atoli]

First, about Atomos:
I think Atomos is something actually GOOD for us.
Remember how nobody actually asked us to kill Atomos? Different from the primals like Ifrit, different from the Garleans everywhere, especially Darnus?
And how Atomos is native to the Void, a place not bound by time or space?
Also, remember what happened to us adventurers who were saved by Louisoix? We were "sent beyond the reach of time" to wait until the time was ready to come back to Eorzea. Pretty obvious similarity.
I think Atomos was called as a portal to the Void where we were sent. Or at least to make it possible in some way for Louisoix to send us there.

About Bahamut:
He's a primal. Even if we don't do ANYTHING he will vanish after a while because he ate up all the aether around and will have to rest until new energy is available. We know that much from Ifrit and Garuda.
The maze doesn't have to be a place where he sits around all day. It could just be the place where he WILL appear when he has enough energy/aether gathered. Other summons had their special places too (like Garuda's Howling Eye).

The reason why Eorzea isn't totally shriveled up, dead and empty for all eternity is probably because large amounts of aether were evacuated the same way we were - sent into the Void after Atomos took it.
Shortly before the end of 1.0 pretty much all aetherytes were eaten up by him.
Without his energy source Bahamut couldn't go on, vanished, the other Archons called everything back from the Void and everyone started to rebuild our land.
But now (ARR) that aether is back in this world, Bahamut can gather it again and could go on another rampage after he gathered enough. That's why alliances of adventurers go into his maze to stop that from happening by finally sealing him again (which would be the reason why the keys that dropped from Dalamud will be needed in the maze, as explained in the liveletter).

A lot of speculation, sure, but I think the pieces fit neatly together
Few other explanations make sense if you don't go the "alternate universe/timeline" way.

Yeahh, thats why i thought it will be better that we were sent to the past rather than to the future to kill Bahamut before it destroys Eorzea

That's not making any sense. We already WERE in the past and failed to stop it from destroying Eorzea.
Sending us to the past to fail again and again would be pointless.