It didn't really occur to me until I did a run-through of Amaurot in explorer mode, but I now cannot help but question whether or not there is some connection between that ominous, glowing red haze you can see hanging over the world at the end of the dungeon and the similar substance the towers seem to be sending into the sky.
Though more important is the question of what it is. Some kind of aetherial "pollution" generated as a side effect of summoning/creation magicks, perhaps?
I'm also starting to think that Zodiark may not actually be involved in the return of the Final Days and his awakening may simply end up being in response to that, seeing as it's the very reason he was brought into existence in the first place.