Could you maybe extend the no_build_in ignoring to all vanilla hullmods, not just SO?
Neural Interface & Integrator - yeah, probably. I don't see much of a downside to this, but then again, I never use those two.
Phase Anchor - I need to think about it. My knee-jerk reaction was "no, robbing the player of its once-per-battle effect and control over it would be bad and annoying". I don't mind the mod ruining some ships by giving them nonsensical loadouts, but interfering with other ships is a bit too much for my taste. The real question is whether anybody actually cares about the emergency phase.
Shield Shunt - just to see the world burn? Maybe with a very low weight it wouldn't get too old too quick. It's a borderline d-mod for many ships
Also found a minor "bug" - Recovery Shuttles can occur on ships with built-in drone wings (Tempest, Venture, etc), where it does nothing (no crew losses with drones to begin with).
Hardly an elegant solution, but I can make the mod consider ship's variant. Has some meme potential too.