What's the point with that quite lackluster story in Endwalker?

[MikkoAkure]

Well, this is awkward

I don't get how this is difficult to understand.

Hydaelyn's summoning contrasts against Zodiark's because he kept the souls of those sacrificed intact. As we know, Hydaelyn did not. Eulogia says "fragments of our former souls", which if my understanding of English is correct doesn't mean a whole soul.

We already knew before this patch that The Watcher had vague memories from his other life and that two Ancients in Elpis were likely Althyk and Nymeia because the latter has the exact same line in Elpis and in the raids (confirmed at the end, and something Venat could not possibly have known to be able to repeat). So we had a reasonable suspicion that the gods were based on Venat's supporters.

It wasn't a great leap of logic even back then to suggest that The Twelve plus One were created from bits of remaining fragmented soul as the cores of the creation magic used to bring them to "life" and grant them a semblance of personality of their former selves. They're still mostly just advanced programming other than that. It doesn't contradict anything.