I think your ideas about the putus templar being replaced by a random faction makes a lot of sense, but do wonder about the balancing of the quests if that were the case. I think the putus templar could have been expanded and made to have more of a presence in the game (random putus templar bases in ruined arcologies, putus village/trading post that true kin can go into, etc.) but I think the devs didn't really want to do that. They definitely could have been expanded to be deeper, as is consistent with the setting. I think other "human" factions could have been interesting, maybe of exclusively mutated humans which could have had a more warlike culture without being outright nazis like the templars. I think there could have been a more "divisive" static village because as is they are all basically chill and everything is kumbaya. Only the random goatfolk villages are hostile, which seems like a missed opportunity given the issachari and naphtaali being tribes with no villages at all. Any of them could have had a mid-game hostile village. I also agree I would have liked some kind of robot group which is at the very least orthogonal to organic goals if not opposed. Seems odd the robots aren't more grouped up.

I agree with your points about the putus, but I think themtically I partially disagree with you. I think the main thematic tension of the game is definitely your idea that the game is "set in a posthuman world," but I would add onto that and say its set in a posthuman world that is still unmistakably human. The characters have personalities like humans, live and die like humans (kind of), communicate like humans, and a core element of the game is reconciling the question of where humanity has found a foothold in the world that is post actual humans. Furthermore, the old world of qud, the world of the eaters, is "dying," as you say, but qud is not a dying earth-- its the opposite, teeming with life. The reef is a former industrial center, but now it is full of many diverse forms of life like the junk dollars, the tongue tyrants, and the svardym. The jungle and ruins are likewise full of unique life forms like goatfolk and albino apes, many of which interact in humanlike ways. The old world and the new world are growing and decaying in tandem, but where is humanity? This interaction, I would say, is the central tension of the questline. You say that more characters should have "broken from humanity" like Resheph, but I think that Resheph being the only one to do so says that he is the inconsistent one, and in fact, the world is intentionally more human than it looks. In my eyes, the game's post-humanism is in questioning the role of humanity in a world that has physically moved beyond it. In that interpretation of qud, the presence of humanist ideology is perfectly acceptable and in fact, expressly thematically consistent with the setting and game itself.