Unfortunately, CT was written completely ignorant to the existence of Azys Lla, so certain answers it provided that worked at the time don't really work as well now, or require tremendous leaps to fill gaps in the lore, like myahele's post above. Also, a lot happens that wouldn't have flown at the time if parties concerned were aware of another death fortress still out there somewhere. How many infinite power sources does one need to destroy the world, that Dalamud would need to be built after sealing the Triad?

But I have other bones to pick with that storyline, so ignore me.