Yeah... the game really should go more into aether-theory somewhere (Sidequests in the expansion that has Sharlayan anyone?). The entire first section of the Lore Book is all about Aether science, the structure of Hydalyen the star/planet, Hydalyen and Zodiark's relationship, the Twelve and the Heavens and Hells. The book treats them like they're all part of the same system, or at the very least have something important to do with each other. Said system goes back at least to the Allagans (for all their science, they did worship the Twelve; this is the civilization that gave Eorzea the deck the Astrologins still use, etc.). It actually goes back further as magic stemmed from religion, not the other way around, in the 2nd Astral Era. However, we haven't really seen anything in all this time (fives Astral/Umbra eras since) to disprove that those ideas are incorrect.

I highly doubt any of the fundamental rules are going to change any time soon. Or revealed to have been false this entire time. Too much of the game assumes the characters and players are familiar with how the system roughly works to pull the rug out from under us three expansions in. It's one thing to put information we've gleaned from various places in it's proper place, it's another to say it was wrong.