One possible reasoning is that AI cores are illegal, salvaged ships under human control are not. Certainly the Hegemony doesn't seem to complain when you're flying around in irreplaceable Legion XIVs.
And it's much harder to tell if that Radiant or Glimmer has been refit for a human bridge crew (potentially a remote from different ship bridge crew like Neural Interface) or if it's actually being run by an illegal Alpha core without doing an in depth inspection. Since it's possible to run the ships without any AI cores at all, that's presumably the standard assumption, in the same way planets are assumed not to have AI cores unless they find evidence.
Although a Hegemony AI inspection fleet for ships instead of planets, if you're running automated ships, might be a cool one off story encounter. Just checking to make sure the main character isn't an Alpha core or some such. I mean, they are a little too competent if you know what I mean?
The thing about the Ziggurat is it contains unique, alien and unknown tech. From the descriptions it sounds like the Tri-tachyon scientists didn't really know what they were messing with. Radiants however, are just known technology, scaled up a bit through clever engineering. Phase skimmers are used by pirates even, just not on capitals. And all the other automated ships use well understood technology, even if they might be a little bit better put together. If Tri-tachyon came out and started selling <Redacted> looking ships with human crew accommodations, no one would care most likely. It's like them selling Paragons, Hyperions, and Dooms. High tech, sure, but start a fight randomly high enough tech? Not really. If you want one, just buy it from Tri-tachyon.
And if a faction wants a Radiant to dissect, well they can hire an enterprising mercenary captain for half a million credits to go out and blow up a fleet for them via a contact, then swoop in later with a discrete and brave salvage crew. I mean, why else are they hiring you to do that, when <Redacted> don't leave their star systems normally.