"Any sufficiently advanced technology is indistinguishable from magic." - Arthur C. Clarke
I assume that's what the descriptions are going for.
AI is infinitely more suited to space than meatbags, not hard to see why. Just think of the difference between our ability to send probes vs. manned missions to outer space currently. So it's not surprising they could thrive in many places where humans don't have the resources to. Like Schwartz said, it's actually surprising how weak the Remnants are, considering that Alpha cores are explicitly stated to be superhumanly intelligent and the Remnant are by far the largest faction by number of systems "colonized" in the sector. They've had more than 100 years to develop their technology, too, and have advanced (if we assume the omega are the remnant 2.0), unlike the rest of the sector.
AI cognition could potentially be on the order of ten million times faster than human cognition, going just by conduction velocity, and there is no known reason why self-improving artificial intelligence could not become qualitatively "superior" intelligence, and not just faster, too. You actually need some hand-waving like inherent limits to artificial intelligence's ability to replicate human abilities, or that AI systems are very difficult to construct and maintain even for the AI themselves, to explain why humans could fight superhuman AI at all in any sci-fi-setting that contains significant numbers of hostile superhuman artificial intelligences.
It's very easy to see how AI could go out of control and how AI could create things beyond the understanding of its creators. If you assume the AI has superior intelligence like is explicitly stated in the Starsector setting for alpha level AI, then that implies that it can understand/reason about at least some things that its creators cannot, since otherwise it would have exactly the same limitations as its creators, which is contradictory if it is of superior intelligence.
Also, they might just be disinterested in the core systems, since if they want e.g. metal they can just mine it from an asteroid in one of their systems without the asteroid shooting back. Could just be more resource efficient for the time being to let the meatbags have their systems and colonize the rest of the sector. Habitable worlds and human-made structures might not be particularly valuable to them, they might for example prefer extreme cold due to alpha cores being described as generating a lot of heat. Where their ships come from when they seem to have no mining operations or planetside operations seems unexplained, though. Clearly they are making more ships and are not currently waging war, since they keep to their systems, have an infinite number of fleets and the player can't wipe them out from a system in most cases. Maybe we are supposed to assume they are generally dormant with some exceptions, but then where do the new ships come from.
The best explanation for their weakness to me would be that maybe only a few AI controlled ships remained after the war, and they've taken their time to multiply, like an infection starting from only a few bacteria, only just recently reaching noticeable numbers just before the player's arrival. Of course this explanation also means AI apocalypse is imminent unless they are stopped immediately.