I always imagined the sound being related to a FFXIV version of Jenova somehow. Hear me out. There are reason why I think this, though it is based on my limited memory of FFVII, so things may be wrong.
In FFVII, Jenova is referred to as a 'Calamity'. Jenova descended to the planet Gaia via a meteorite, and infected many Cetra, referred to as 'Ancients', turning them into monsters. Jenova almost wiped out all of the Ancients, and was only able to be sealed in the northern crater by the few surviving Ancients, who eventually died themselves.
Now, notice the similarities here. Jenova, the Calamity, descending in a meteor, or star shower, destroying the Cetra, the ones known as the 'Ancients'. Sound familiar?
It's my belief that in FFXIV, the 'sound' was created by some fell creature that descended from the sky. The Sound the creature made infected the Ancients, turning their own creation magic against them, giving birth to the terrible monsters we saw in Amourot, just as Jenova infected the Ancients of Gaia. Or perhaps it wasn't the creature, but the planet itself 'moaning' in pain from being infected by this alien parasite monster.
Either way, the similarities are there, or at least in my mind.