It works via a submarket the player has to deliver ships to, so that's already covered. The issue is that there are obtainable, non unique ships out there that would break the game if the player could produce them - Templars, for instance.
About white list - maybe you made it possible for player to add ships to white list too? For example if someone really wants to got BB blueprints this way - why not? This is a single player sandbox anyway.
About limitation - I think one of valid option is adding chance to succeed. Maybe based on player tech skill three and\or AI core attached to industry? And if you fail - you just lost hull for nothing. I know for some people this will be extremely frustrating even with 5% chance to fail, but this can be fixed with simple "made reverse-engeneering have 100% chance to succeed no matter what" option in settings.
1) the player can manually whitelist any ship he wants via .csv edits.
2)penalizing the player for using a feature depending on RNG is a good way to make sure no one will ever use it.
Mechanics for this are already done, give it a try once it releases!
In any case, this is super offtopic for this thread, apologies for that. I just wanted to make sure you don't put work into something that would be released somewhere else in the near future.