Ok, I just realized.
People clearly survived the Great Flood and that Qarn may have been built by Mhachi survivors. We also heard that people hunted down mages during the Water Umbral era.
What I don't understand is why make an flying Ark and put themselves in these stasis pods if their goal is to escape the great flood calamity? Having a flying vessel means that they can go where ever they wanted, so something went wrong.
Maybe in desperation they went into the Void itself and that something went wrong while they were inside the void?
If you look at the surface of the ark, it kinda looks like Atomos skin
http://img1.wikia.nocookie.net/__cb2...mos_(FFXI).png