The "Universal Aether Farm for Zodiark" plan is actually a bit contentious with what we learned in Endwalker. The scene showing the Sundering, even if not taken literally, shows Venat doing so to stop her fellows from committing suicide in Zodiark's name, not declaring their intent to cultivate life to sacrifice. They had given up on the future and only sought solace in the "perfect paradise" of the past, regardless of the price that had to be paid to achieve that.

"But the past we loved is not the future you seek. That is why we fought. And why I lost." So sayeth Emet-Selch, even if he refuses to compromise his ideals.

Anyway, in regards to Hydaelyn, well... there were fewer souls making her up, and she still had her original "heart" (e.g. Venat). Zodiark has many souls within him but without a guiding will he's just a creature of instinct, which is why Danny Boy hijacks him to fight us.

In response to OP's question... the seat of Azem existed long before the Final Days. Venat was the previous Azem and "our" Azem's mentor, who left the seat but did not return to the star (or less euphemistically, commit ritual suicide) until we defeated her as Hydaelyn deep within the Aetherial Sea. "Our" Azem rejected the proposition to summon Zodiark and defected from the Convocation. (Neither did they accept summoning Hydaelyn, though that's a bit of a digression.)