Spoiler
If I had to guess, I'd say the Threat is more of a "Grey Goo" scenario, brought on by some Domain numbnuts that somehow came up with a worse idea than AI to fight their wars for them. Or maybe a response to AI independence and/or Omega and messed up big time.
They're more or less based upon once-existing hull-types, and mentioned to be self-replicating/recycling nanomachines by Zunya. It checks out; fragments wouldn't just come from nothing and require raw material, that material being manufactured goods/shiphulls, "organic components," whatever they can process from mining planets. Not to mention many rogue planet surveys turn up Ruined Infrastructure, but never explorable ruins (no idea if this is just a quirk of my modlist.) Tells me they strip away whatever is useful and leave nothing but the barest of bones, after the coast is clear.
imo The Threat has been systematically assimilating whatever they come across, haven't gotten around to making the Sector lunch, and we're too busy in-fighting to bother with expensive expeditions into the peripherals. Zunya clearly knows something more, but not enough, and just doesn't have enough clout to do much more than pay reckless fleet captains to bring back ANYTHING for more intel. This would also go same for the highest levels of TT. She's a sociopath, all corporate overlords are, and at the end of the day sociopaths are always in it for themselves and their goals. Just letting the Threat eat them as well as those that contribute to their profit margins or longevity wouldn't be in the Company's best interests.
Besides the Dwellers, Starsector is a fairly grounded sci-fi setting. Just saying "the Threat is aliens" would be lazy, and calling them a cognitohazard wouldn't be as grounded and feel like an SCP ripoff. The writers are not lazy or unimaginative.
This has turned into something close to a wool-gathering essay so I'm gonna leave it here: the cynical pursuit and maintenance of profit by any means necessary is a core gameplay mechanic. Selling drugs, harvesting organs, looting anything not nailed down, war-profiteering, manufacturing conflict for the purpose of profiteering, undercutting and hamstringing competitors without removing them outright. Charity is a fool's errand. For example, I'm not taking 5,000 credits to transport a bunch of Luddic Pilgrims to some shrine that'll cost 10,000 in supply and fuel.
The AI Remnant don't care for credits, only threaten future investments, and thus must be eliminated. Their struggle for existence is irrelevant to that. The Threat is similar in that regard, only they're a programmed machine produced to combat a thinking machine, and they've gone even more off the rails.
I'm more inclined to believe that there is a message unfolding here, and it's not a kind one. The profitable banality of evil rather than the cooperative human spirit would be the Sector's best bet against a manufactured human mistake.