I do believe the Progenitors will become a cautionary tale, of sorts.
But I believe, firmly, that the Progenitors are artificial intelligence.
Given Bakker's predilection for the subject and view of its inevitability and culture/species-warping potential, it seems logical, and what he would see as the inevitable end to the "death of meaning" and identification of the universe as an entirely mechanical process. Without moral meaning, we're back to Nietzsche's "good v. bad" supplanting "good v. evil," and AI is already outperforming human intellect at most tasks in our world, before we've even developed a true AI. We know them capable of it from the Ark's machine intelligence.
The question for me is, were they entirely AI prior to finding damnation is factual, or subsequently? If the former, it could be the inherent reason for their damnation; mechanistic souls utterly divorced from semantics, strictly pursuing intentional amoral goals. If the latter, one could assume the Progenitors, having already developed AI distinct from themselves, sought to copy their souls/consciousness into the superior form to forestall damnation (their homeworld being entirely anarcane ground, any solution is entirely reliant upon the Tekne). Side-stepping the issue seems to be most species' go-to move in the absence of a means to end it, or to wait out the interim until success.
Given the worries regarding our own future's technological advances in light of a meritocratic capitalist economy, one might also assume the AI-Progenitors came from wealthy supermen who rode the transhumanist wave to its logical conclusion, and the Inchoroi are the dead-end of the working poor, genetically and neurologically altered for maximum utility to the holders of wealth over the course of time. (Wire up the brain so carnal reward is the ultimate, reward them with this upon task completion.)
I'm pretty sure they were fleshy beings, as described by the way the cast aside their Gods and temples etc., remolded themselves to plunge deeper perversions (have a hard time seeing a piece of software doing this). Also, I think Bakker's fear of AI is not so much related to humans becoming AI but the way AI can exploit human cheat space in this newly arising cognitive ecology. Also, I'm just gonna say that I personally find strong AI to be a fantasy. Teaching computers how to make a good statistical model of some data is a far shot away from something that even thinks like a human, even though it may be way better than humans at specific tasks.
Also, regarding the capitalism/class thing
Nothing was forbidden them, short the obstruction of others and their desires
It looks more like socialism to me!
Another question is, are hedonism and sociopathy really inevitable?
Probably, but hedonism might not be hedonism to the hedonist, only from our perspective. Hell, you could argue a man undergoing hormone therapy and surgery to look like a woman isn't far off from "regrafting themselves to plunge ever deeper perversions".
But morals are not universally shared or constant through time.
Well, they basically have been for 2 millennia. Things change, sure. But, for the most part I don't see the horror story that so many warn us of, coming to pass. Its in a nature to want to be good people, please others, make others think highly of us. To do this, you have to follow morals. I don't see that changing. In fact, my opinion of what science will do to us, is make a better us. I feel that at some point (not in my lifetime, for sure), humanity will wake up and look for common good for each other. It'll take something awful to happen, but I believe it will.
They haven't. In a span of a few short years homosexuality has become accepted, maybe even celebrated, in the West, after a long period of harsh discrimination. Also, as much as it lies in our nature to be good to the good, it's also natural for us to want to punish the evil. The problem is that good and evil are not fixed, at all.
There are many books, movies and such on this very subject. When we become so advanced the majority of population isnt needed, what do we become? Its explored in The Expanse.
To be honest I don't think this is going to happen. At some point, somebody, probably the Chinese or something, will say "fuck your shitty arbitrary and hypocritical morals, I'm going to gene-edit this baby and try making it more intelligent", and voila.