If I pilot those ships, I would not want Heavy Armor because it hurts turning speed. I put Heavy Armor on Onslaught once recently, and it was too sluggish at turning. I guess it needs Auxiliary Thrusters, but taking both means not enough OP left for other stuff.
Auxiliary Thrusters is nice, but the OP cost is high enough that I cannot afford it. I generally rely on skills to give turning speed.
If I have slow turning weapons, like heavier autocannons, Hellbore, or Gauss, I probably would not want Armored Weapon Mounts. At least not without Advanced Turret Gyros.
I would take Resistant Flux Coils just to vent faster, if I think I may pilot the ship. EMP protection is good too.
Automated Repair Unit combined with Damage Control 2 is very nice. With both, weapons and engines repair quickly enough that it does not matter much if they get knocked out.
I would get Reinforced Bulkheads mainly for the guaranteed recovery after battle (if ship has no officer), especially if they were clunkers to begin with. More hp is nice, but secondary.
If I want a built-in hullmod for Onslaught/Dominator, it would be Expanded Missile Racks. That hullmod is expensive, and they need missiles to fight well early.