There is a useless option in the autofit screen:
Always add "<useless hullmod>"
Umm, you
do realize what Reinforced Bulkheads does, right? And why it's something you might want on every single ship you own?
Hint: It means you have a waaaaaay better chance to recover the ship if it's destroyed in combat. That's a pretty damn important thing to have if you ask me, and probably the single most sensible hullmod to take its place in the "Always add..." Autofit option.
If that's not important to you for whatever reasons, then uncheck it.
Most of the rest of your suggestions wouldn't work because either they make too specialized a role (ie. they're not something you'd want on every ship so why the hell would anyone ever check it?) or they're not a hullmod the player has access to right from the start of a campaign game.
EDIT: On the flipside, the only two hullmods I could think of having a "Always add..." checkbox would be ITU since it's usually a must-have for cruisers and capitals (and some destroyers - although you do have to find it first) and Safety Overrides, since people do thematic playthroughs with SO on every ship.