Can also add the quest allowing the ship to be looted seems to be bugged, or at least, isn't consistent. You can luckily just use the Console Command mod to add it in though.
I do not think it is bugged, it's just that we are spoiled by the other mod makers who wrote code to ensure that their bounty ships drop as derelicts. I do not know how to do this, so for now I recommend using console commands.
I don't know if this is known. As of this moment the big 3 BP's you can get do not add all the ships. using all three you only get the battleship yoshura as a capital and you don't get the carrier or anything else i know some of its mission stuff but the horizon BP only adds like 3 ships the enigma BP only adds weapons and the archon BP gives the BB but none of the other caps. it seems to give most of the rest of the classes just the capitals i noticed.
although I am only the translator for this mod, I do not think it is unusual for ships to be unavailable from the factions big ship blueprints. For example, in diable, I believe the Maelstrom and the Pandemonium are unavailable. If you want those blueprints you can raid for them.
the bigger question is how to get the Azmodaeus and the Vatican Mk.II, which in the files are "no_drop, no_bp_drop, restricted" because I don't think I've ever seen them. Are they even in the game?