Re: Bug
Its a vanilla bug that should be fixed in the next vanilla update. I can technically fix it now but then I'd be doing triple work so I am leaving it alone.
Re: Derelicts
You can recover the Guardian if you go to the mod settings and set "capturableGuardian":false, to "capturableGuardian":true,
I'll see about letting Derelicts be recoverable with the skill too. That won't need a setting honestly. I'm glad the Mothership is a more interesting fight now.

Re: Radiants and Brilliants
Nice its good to know that the endgame content is as scary as it should be! You will need good weapons and builds, and high level officers/mercenaries to beat them I'd imagine. If you read the response to Ranakastrasz, I'd also recommend bringing ship builds that compliment each other. Using defensive hullmods and flux free weapons can create linebacker ships which you can support with long range support ships and high alpha-strike capable ships. Think of it like swordsmen/pikemen creating a defensive line supported by rear archers and flanking light or heavy cavalry.
Even with all of that, I'd expect to still take losses and you should bring a large fleet to provide reinforcements. Radiants in particular are very, very powerful ships that will shred through battle lines when its ship system is active. I'd suggest waiting until you have several self-sufficient colonies as money-generating platform from which to reproduce your fleets after raiding REDACTED systems before seriously attempting that kind of content.
Re: Ship Trophies
Now that there is a much wider variety of "faction-less" ships available, I am going to remove faction ship trophies at some point (probably with an optional setting that defaults to true since I know some people don't like the idea). Then faction ships will only be available on military markets and will require good reputation/commissions to require.
The other way you will be able to get them will be finding/raiding their blueprints and producing them at your colonies, or getting them through contacts.
The reason I am going this route is A) I like the sense of progression from unlocking unique, thematic ships as you get deeper into a campaign and B) as you describe it is currently way too easy to follow NPC fleets around until their is a battle and then looting the spoils without any real challenge involved except RNG. I generally don't like RNG like that and the only real exception I've made is with the blueprint system - since it varies playthroughs enough to provide a lot of replay-ability for the mod.