IIRC, it's a minor plot point in Endwalker that the Ancients weren't aware that the Final Days could cause a transformation instead of a forced summoning in beings with low dynamis, which suggests that everyone experiencing the Final Days back then could also use creation magic. Maybe? I dunno, it often doesn't feel like the FFXIV writers fully think these things through.
You could certainly argue against the Rejoinings on a utilitarian basis insofar as they cause tremendous present-day suffering in pursuit of hypothetical future happiness. If it was as simple as snapping your fingers and reaffixing everyone's souls to original counterpart, not so much, but.
I think it's pretty obvious that FFXIV has a bone to pick with hedonism in general, but what's frustrating about it to me isn't that it has this opinion - there's nothing wrong with a piece of art expressing a moral philosophy I don't agree with - but rather that it treats it as something self-evidently bad rather than really engaging with the question seriously. It deontologically regards the abundance of life as the utmost good for its own sake, but only really makes emotional arguments in justifying this premise, like Venat's "lands that stretched on forever" speech. And it caricatures its ethical opposition rather than actually countering their points substantially; for the Plenty civilization, which pursued optimal happiness over all else, the author simply invents a fantastical basis for why this is bad which ends up making them all kill themselves... Or in the other direction, Meteion, the closest thing to an anti-natalist counterargument to the perspective, is framed as a depressed victim who doesn't even really mean the ideology she espouses. (That's not to say I dislike Meteion as a villain; I was actually reasonably fond of her, but she obviously isn't intended as represent any kind of substantial antithesis.)
But despite that lack of substance, anything other than deference to its perspective is presented as a kind of immaturity. Despite the fact that the Ancients clamoring for their civilization to be restored at the potential long-term expense of future life emerging in the universe being pretty reasonable from a lot of moral perspectives, this is conceptualized as a kind of original sin; self-evidently bad.
This is one of the ways Endwalker frustrated me the most. I felt like I was being talked down to because it prosthelytized rather than argued.