Just some other things to point out.
The Ancients did not solely reside in Amaurot. The Amaurotines knew in advance what "The Final Days" entailed, as you can find out about it during the quests, and is why the Conclave was working on the plans for Zodiark in the city's timeframe. The Screeching sound that begot the disaster is said to "wrest control of" the Ancients' creation magicks, after which things began to spiral out of control. Focused creation, as with Zodiark, was still possible.