Did I skip something in the MSQ? This part doesn't make any sense to me

[Jojoya]

I don't know if I misunderstood what you meant, but there was the couple during the gondola quest. The Elezen man tells us even though he died and the woman he loved forgot who he was, she never married anyone else, and felt a sense of loss. It's implied that she remembers him now, and we see them happy after he proposes to her on the bridge.

Correct. We met him and he died before she did. We never met her but he acknowledges that she had no memory of him after his death during her life. The computer running Living Memory would have had to restore her memories of him for their meeting there (the memories the living have of the newly departed presumably being uploaded into the "cloud" when the other person died), and Cahciua even tells us that the computer was know to manipulate what memories the Endless have access to.

Again, there's some really bad writing going on and some of it is at odds with things that were explained in prior expansions. Trying to nitpick philosophical points is rather useless when it's a fictional story and the writers are the ones that control what is going on.

The writers created the Endless as computer facsimiles of dead people based on the memories stripped from their souls and so that's all they are. The intended moral appears to be "it is wrong to kill the living for the sake of those already dead", which does more or less align with one of the morals at the core of the Hydaelyn/Zodiark story.

It doesn't matter how much players wants to convince themselves the Endless are living beings. The writers have told us that they are not and it is the writers that have created the Endless.

G'raha and Krile both exclaimed that the Alexandrians were performing the same exact process with souls that the planet itself does with the aetherial sea. If that was the case, why didn't the Alexandrians just tap into their own aetherial sea and just keep cycling souls like the planet already does? Nothing is actually being expended, just cycled. But I guess we overlook massive lore contradictions and plot holes like that

Except the Aetherial Sea uses the "recycled" soul to create a new person. We also know that there's a process that can create new souls though we have no idea how that happens or if the Aetherial Sea is involved.

The Alexandrians use it to either revive a dead person or or preserve someone's memory. There definitely are souls expended when there is no new life created. We get no explanation for what happens to the portion of the soul expended for either of those purposes.

This reminds me of another question I had doing MSQ. Why are resonators are only to revive those who die in accidents and not those who die of illness/old age? How do the bodies of those revived apparently get instantly healed of all wounds? Their bodies should be in the same state as they were at time of death, causing them to die again almost instantly since it is only the soul being restored, not the body replaced.

More bad writing unless it eventually gets revealed that no one in Alexandria is alive and they're all dead facsimiles whether they know it or not.