Functionally, while the stinger at the end is a big shock, it doesn't change much. As long as Hydaelyn remains in the aetherial realm, any aether drain she may have as a result of being a primal should be nonexistent. Her tempering also appears to be benign, insofar as it doesn't compel us to do anything the same way most primals' tempering makes others into slavish devotees (this may or may not be a consequence of the Ascian ritual used to summon most contemporary primals).
However, let's compile the hints we have so far to the true nature of the world.
Ramuh's conjecture: Light and darkness were once indistinguishable, but darkness came from the hearts of men.
Lahabrea's account: Hydaelyn is a parasite responsible for warping the natural and aetheric laws of the world, and must be burned out to repair potential damage to the world.
Hydaelyn's account: She and Zodiark once dwelt as one in the aetherial sea until Zodiark began to covet power, threatening the balance; in order to mitigate any damage he may have caused in seeking said power, Hydaelyn banished Zodiark as the moon, shattering his power into thirteen pieces which became the Reflections.
Varis: recreate the "original, perfect master race" from before the Sundering (to kill the Ascians).
Solus' (Emet-Selch's) account: Hydaelyn and Zodiark are both primals.
Cave painting inference: Hydaelyn and Zodiark are two halves of one twilight / dawn god(dess).
I think I get it, but... I'm not really sure how we're supposed to resolve all this.