If I may ask, what's the real design goal of lockdown protocol?
You may always ask/debate. Feedback helps the mod get better.

Its a trial run of a slew of design intentions with this overall goal: Make faction commissions very unique and create more replay-ability along those sorts of lines.
There is already replay-ability each playthrough simply with the proc gen, but for the most part you can get access to the ships you want without much consideration into choosing to ally with a faction or not. Allying with a faction is more about credits. That is because you can harvest ships off enemy fleets or wait for npc campaign skirmishes to salvage whats left behind in the wreckage. Its mostly up to RNG. Similarly, blueprints come down to salvage RNG and raiding for what you are unlucky enough to not find.
I had desired to lock out or reduce that RNG in the case of ships (already made tiers of blueprint rarity that makes high end blueprints more rare), while opening up the accessibility of ships when getting commissioned by a faction through blueprint packages rewarded at the time of commission.
To me, this makes the choice of which faction, if any, to ally with more interesting. What is your goal this playthrough? Advanced and powerful ships and weapons? Tri-Tachyon, Sci-Corps, Archean Order or Adamantine Consortium are good choices and each specialize in something different with their own flavor, motivations and political implications.
Money and salvage boosts more your style? Pirates and Trader Guilds will make strong choices for that. (Not yet implemented)
Political influence or otherwise throwing your weight around to get faction aid appealing? Hegemony or Luddic Church gives those kinds of perks (Not yet implemented) alongside access to their custom ships and weapons that have their own strengths/drawbacks.
So, to summarize:
The intent was to further emphasize and make more interesting the choice of faction alignment. Since it is half-baked at the moment, and the derelict complication is probably not worth the effort for now while I work on more lore-related things, I'll likely remove it until I can get more pieces of the puzzle working.
Right now, it admittedly feels a little more punishing than anticipated since the flavor of faction choice is only halfway implemented and certain features that are designed to hook into those perks aren't developed yet.