I honestly never read it as 'the souls fell out and are in the aetherial sea'; the third sacrifice was a confirmed element as far back as 5.0, and that particular part only really makes sense if there are souls still in there. After all, we heard the tale from Emet (and Fake Hythlodaeus, who's basically an extension of such for these purposes); he knows and accepts how the life cycle works, so he wouldn't be so torn up over this unless it wasn't working as he expects it to. So yeah, them still being in there, and the Ascians being the only ones with a plan to get them out of there, seems to be how the story was always intended to work, it was just made explicit rather than remaining clearly implied. I've always had the question of if Zodiark was powered by souls or merely aether, but that's really just a semantic difference given that they were sacrificing lives to it anyway; the answer doesn't matter and would change nothing.
I think the core thing we learned about those guys in Endwalker wasn't actually related to the situation going on around them--none of that really seemed to change, although the context was colored in more--and more about what it's like in there. The fact that they seemed to be conscious up until the point of the sundering, and then 'drifted into a waking dream' until the events around when we turned up. Their general mental state, too, was news: that only one actually seems to regret their sacrifice, and the rest are more mourning--depending on the individual--either the fact it had to happen, or the fact that it doesn't seem to be working. (Or are Hythlodaeus, who seems kinda just okay with it.) In fiction, one person's story trumps a swathe of just plain facts, so I will note that that one guy was probably representative of a larger group of regretful people in there, but he was a minority even among the people we did hear from. Most of them seemed content with their sacrifice, they just wish it worked.
EDIT: All of this is to say, yeah, the writers wrote this, but they wrote this with intention and reason; it accentuates the tragedy of both the sacrifices and the Ascians, as well as an irony that the third sacrifice was all for the purposes of returning people who, for the most part, didn't want their sacrifice undone.