Some new observations. . .
Can you give #3 a try again, but leave them Trans-Newtonian technology? It might be that's the gate tech they need to behave like a TN NPR. They'll be "technically" Trans-Newtonian, but still have to research all the other tech. No guarantees, just something to try.
Tried it, and it didn't work. More precisely: I created a new NPR race, deleted all their non-conventional technologies (in other words, I copy/pasted a conventional technology set over theirs in the proper database table, and deleted redundant lines), switched the race to a player race, then gave them TN Technology via the "Instant" button, and switched them back to an NPR. The NPR didn't work, they just sat there.
However!
Then I added technologies to get them back to TN-starting levels. At that moment, the NPR started working again! This suggest that the AI does indeed need certain minimal technologies to be able to operate. I'm trying to find the minimal set but it's very probable these need to be all the TN starting technologies.
Also. . . this only works if a race were generated as an TN-able NPR from the start up. If I generate them as conventional player race, and only then switch them to an NPR, they won't do anything no matter what technologies I give them. This is unfortunate, because raced generated as TN-able NPRs will already have some ship components researched - I can get rid of them, but it's a hassle. In any case, it seems that the NPR generation creates certain entries in the database that a player-race generation doesn't. I'm still not 100% sure about this because I haven't really done repeated, controlled attempts, but it sounds quite logical.
So yeah, at this point it seems a conventional NPR isn't possible. What works fine is an NPR with only conventional industry but with the most basic TN technology already researched.