... reasons for why permanently building SO into a hull could, perhaps, be a bit ill-advised...
(I think I was being a bit too subtle here...)
I mean adding ill-advised modification hullmod is an option (like how all Luddic ships have with their SO) when you permanently build in SO, but doesn't that just bring in more RNG mechanics regarding when and how things break down? I'd assume that means preventing ill-advised from being removed with restoration as well on Luddic ships?
I'd almost suggest if a hull mod is above a certain value for the ship class, the maximum OP simply gets decreased. Build in safety overrides on a cruiser, and maybe 15 off max OP (essentially making the maximum discount 30 OP). This also means it can cleanly work with potential non-vanilla hull mods which are expensive but do crazy things, as opposed to having a targeted single hull mod fix. It also means if you come up with ideas for other really expensive hull mods, you don't have to come up with individual targeted fixes. Also, if you set the point low enough, then Hardened shields doesn't become must be built in on every high tech ship (at 30 points, it's pretty much a no brainer. If max discount was effectively 25 OP on a cruiser, then other things might get built in).
Take my current SO aurora. SO, Hardened Subsystems, Hardened Shields are all built in. I also have expanded missile racks and Shield Conversion - Front. If building in SO has a disadvantage worth more than 15 OP (which I consider ill-advised as meeting), I'm just going to build in Expanded Missiles and place SO normally. It's a 25 OP difference, and goes in the right direction, but just feels like an indirect way to do it.
I admit, this does kinda turn story points explicitly into +25 or +30 OP points on a cruiser - but they kinda are that anyways right now.