I know it's been a long time since anyone in this thread had a reply, but seeing as there was no solution present, I had found a solution that really doesn't require a lot of modding expertise.
If you want the blueprints for the Remnant Lux for instance, and you would like to find it while scavenging, you can go to the wing_data.csv in the hulls folder located in C:\Fractal Softworks\Starsector\starsector-core\data\hulls
While you're there, there are a set of words enclosed in "quotation" marks. As an example, the Lux's is:
"no_sell, fighter, remnant, fighter5, auto_fighter, merc"
What we'll do to add it to the lists of salvageable items, and to keep it still rare, we'll add the tag rare_bp to our list of tags.
"no_sell, fighter, rare_bp, remnant, fighter5, auto_fighter, merc"
(Interestingly enough, right below is the Aspect Wing and if you remove no_drop and add rare_bp, you can start producing them. But for your doctrine to effectively equip them, you'd have to add a tag that shows the type of wing and how powerful it should be considered like these three: fighter3, bomber4, or interceptor5)
In the same sense, you can add to the rare blueprints the weapons in weapons.csv and the ships in ship.csv in the same way. So if you wanted your army to field those pesky Unknown weapons, well, only a couple edits away. Interestingly enough, the blueprints seem to be generated so you won't need to actually add any artwork for this to work.
weapon_data.csv location - C:\Fractal Softworks\Starsector\starsector-core\data\weapons
ship_data.csv location - C:\Fractal Softworks\Starsector\starsector-core\data\hulls
wing_data.csv - C:\Fractal Softworks\Starsector\starsector-core\data\hulls
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