The missing mood in the existential horror of the last zone of the game (spoilers)

[Loggos]

We're literally doing what Emet-Selch wanted to do. We're literally going into a world to kill everyone so that we may live. We're told to dehumanize these characters to feel better about it.

Ok I have to admit I strongly disagree with this one. I also thought the story was poop but it was not us who tried to Emet-Selch everyone, it was Sphene. She was an aggressor who tried to conquer new life. She came to our world with the intend to genocide everyone.
We were her victims and had to defend ourselves against her.
Emet didn't defend himself against us like we did against Sphene, we didn't act as aggressors against the Ascians. They attacked us like Sphene.

Coming up with new tech that leads to unnatural outcomes is all fine and good as long as it doesn't encroach on other people's right to live. But if you build something that inherently requires the continuous death of others to sustain itself then you have created a vampiristic system that exceeds the natural resources that exist and that Sphene has to share with everyone.
The endless in that scenario had at least already lived (vs. all the people living for the first time on Eytheris right now). They don't have any right to a prolonged life/eternal life at the cost of everyone else.

This also includes those who died prematurely in Alexandria. People in other reflections die prematurely too. Yet neither they nor Alexandrians have the right to extend their lives by stealing the lives of others.

Emet-Selch of all people had merit in his justification

I really disagree that Emet had merit in his justification but us defending ourselves against interdimensional invaders somehow has not. I thought the Ascians' fate was incredibly sad and I liked the Ancients and their civilisation but they didn't have the right to wipe out 14 worlds after theirs was gone.
(Edit: Sorry for making it sound like you thought Emet is right. I took it like you saying he was wrong but we could still understand his anguish/perspective somehow whereas our actions were wrong but in addition they didn't even warrant this type of understanding we could feel for Emet.)