In Louisoix's own telling of the events he accounts for the aether's source and how it was bestowed upon him.

Originally Posted by
Louisoix
Little choice remained to me. I used the last of my strength to entrust our hope unto the future, and prepared to meet my end. As you have no doubt surmised, I did not perish. When the cage built from the essences of the Twelve was destroyed, the sky was filled with a colossal cloud of aether... This drifting energy responded to the prayers of those fighting below─and to my own desperate wish that the dying realm be saved─by infusing me with the power of a primal. I became the immortal Phoenix, ancient symbol of rebirth.
Of course, that this doesn't
rule out the spires being the Twelve in any way; I'm not trying to say that at all. I just don't find it to be self-evident, either. I'm still in that gray area of "That could have been the true Twelve, but it could just as easily have been man-made artifacts of a half-completed summoning ritual." That's the line of confusion SE want's us to tread, isn't it? They even used that word, again - "essences."
If it was confirmed that
The Twelve just step in and make primals, that'd throw open a lot of doors and slam shut a lot more. We'd need to start a lot of our discussions over again from scratch.