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.)