So I rolled some thoughts around in my head and actually came up with an explanation that lets Chris keep his ships, but has less ooptech, and reconciles a gameplay/lore issue.
First off? The derelicts don't make, refine or collect metal. The derelicts are salvage coordinators, helping your command stations optimize the process of collecting scrap. They're left over from the post-AI War period, when they helped coordinate the recovery of military grade metals. They made one way trips to orbit, and were eventually abandoned in place after the most valuable pieces got picked up. Fast forward to the present, and the devices are more useful than ever because the AI's return means a bunch of new scrap, and no time for it to form metal fields. After all, AIW2 takes place much earlier in its war than Classic does its own. No time for those familiar fields to show up.
The AI can't listen in on human communications this time around, which is why it doesn't bother to destroy the derelicts completely -- they are neither serving a military nor economic purpose that it can tell, and they are not supporting human life. The AI blasts holes in them to stop their signal and moves on. The player's forces don't even need to repair them entirely if Chris wants to keep the damaged ship thing going, since a fully repaired ship represents a possible threat to the AI, while a half repaired weaponless vessel is a curiosity worth exploring much later (though it's still getting blasted).
This is just a lore change, they keep all the same gameplay functions. They produce metal and science under player control, are immobile, don't have weapons, etc. etc. This way toothey can be completely destroyed and rebuilt in game. There just has to be one in place when the player arrives in a system.
Change the name from "derelict" to something more descriptive when it's captured and I'm content. How's this work for everyone else?