I'm curious whether it would be an improvement (compared to the present state, none of this AIP to rebuild stuff) to:
1) make sure all advFact/ASC/fab's seed near the inner grav ring, on a point that maximizes the distance to the nearest wormhole.
2) Have all those, upon being captured, spawn a completely non-repairable (but possibly very slowly self-regenning) stationary "ancient forcefield" that's fairly wide-range, does not reduce outgoing damage, and has a fairly absurd amount of hp (possibly armor too).
You'd still have to deal with Raid Starships, but it could give you a bit of flexibility in dealing with sieges, and some sniper turrets under the ff could mess up raids pretty good.
Though in practice you'd probably just lose them to any major attack anyway, unless I made them really ludicrously durable.