Another source of Aether (Spoilers?)

[Jyera]

Yasyle uses her Crystal of Light to summon Shiva at Azys Lla, so that one is definitely confirmed in-game.

That is a good question about Tupsimati. I was under the impression Papalymo had used it to seal Shinryu, but that still leaves the question of where it is now...

I figured it was consumed and destroyed in the process.