Random thought but would it be reasonable lore-wise for some independent fleets to have the odd Domain or Remnant ship that they had salvaged?
From a gameplay perspective, the player is not punished or is treated any different by patrols or faction stations when docking for having automated ships which give the sense that the Domain and Remnant automated ships are...not exactly an open secret, but one that most experienced starfarers would know about but just don't talk about in the open.
Following on from the same vein, it seems to me that it wouldn't be unreasonable that some other enterprising mercenary captains would also salvage and utilize the occasional drone ship in their fleets as they would need to pay and feed less crew members (and independent explorers/salvagers in particular would make logical sense to do this imo).
If so, a simple addition to the codex entries would also explain their (occasional) use in NPC independent fleets as well as provide some explanation for why the player can freely use them with no in-game repercussions (understanding that this part is almost certainly a QoL thing for the player as otherwise it would be highly disincentivized for the player to even bother with automated ships if they got barred from docking at ports or stopped by patrols for simply having them in their fleets)
"Enterprising captains have been known to salvage and refit automated drones for use in their fleets despite being outlawed across the sector by the Hegemony and Church of Galactic Redemption, however this flagrant disregard of the ban is often overlooked by authorities in the Persean sector without the might of the Domain to back up and enforce these regulations"
