The sea of clouds supposedly has countless small landmasses floating in it that one could build a house on. Stormblood shows a more practical and permanent way of having underwater homes in the Ruby Sea.

The primary issues with Amaurot being a housing zone are the one mentioned earlier that the region it's in was underwater until Bismark created a giant air bubble. Though it shouldn't be an issue for us because of events in Stormblood it would be an issue for any NPC's hired. The other issue is Amaurot is on another shard that from a story point we're just a visitor on and as such we wouldn't be looking for a permanent home there.