I agree. It's understandable that SEEKER's bosses are not made to be recoverable by the player due to obvious reasons (which is good), but it's also sad that they're completely passive and there's absolutely no reason to actually fight them aside from bragging rights and some loot opportunities. I also don't really have an amazing alternative solution how to do it instead.
I personally make some edits in this mod, I added boss ships from Seeker to Remnants, and Cataclyzm and his fleet to Pirates and Luddic Path, although they very rare to sight, and make them recoverable, also I did this with unrecoverable vanilla Guardian and Tesseract too, yes, it makes game easier, but first I just personally not fan of NPC specific stuff, and second, I make them appear in NPC fleets as return.
My main issue with mods what they rarely add Paragon, Aurora, Doom or Tempest power level stuff, and when you have mods with alot weaker stuff, its just bloats game with unneeded content instead of adding variety, because if some stuff is weaker that vanilla, its just makes no sense to use them. I really wish to see more stuff like this, sadly its made only as sprites:
https://imgur.com/a/TSm3iuXAnother thing in Starsector what I personally not much fan off, is endgame, when you get Heavy Industry with alot of blueprints where you can make almost any stuff you want, and really big income, you lost reason to do missions and bounties, and game usually got boring after some time, destroying factions just for reasons still get boring.
Also another problem with Starsector is what world itself somewhat stale, Nex fixes that for some extent, but still, one of examples of games where world feels alive is russian game called Space Ranges, it has common enemy which is with whom all faction fight, and it can destroy all sector without player help, have Rangers NPCs which act like player, take missions, procure equipments etc, text quests which is really interesting compared to Galatia Academy story line which is just plain whole of text, and many of these features I think can be adapted in Starsector. Like common enemy, captains NPC which act like player, takes missions, procure ships, and when killed respawns like player with small fleet.