[Shadowstar]

It's my understanding that it's the crew itself that is the problem. If you take out just the crew quarters you can't build ships because you (and the AI's) have no way to give them crew. You have to modify all vehicles that require crew so that they won't require them anymore, so that you can build them without crew quarters. Then boarding parties should work.

Just building ships with master computers won't stop the AI's from doing it. You effectively have to remove crew from the game entirely. It's actually cleaner than just using master computers since it preserves at least some element of the gameplay formulae created by the difference between live crews and master computer ships.