I put Augmented Engines only on ships that need it to get to burn 9. So my Paragon, and that's it. Unstable Injector goes on ships that are going to be chasing, running away, or that want to get behind the enemy, so my Tempests, Shades, and Civilian ships. My non-Paragon direct combat ships, Medusas and Wolves, I find don't actually need either. They're already mobile enough. I only put Safety Overrides on earlygame Lashers, before I can feasibly go full high-tech. The PPT decrease is just too severe on frigates, the major strength of most of my ship designs is how much they outrange the enemy so SO would actually make them worse, and you can't put SO on capitals or civilian ships. Additionally, the AI really can't handle close-range ships well at all. Long-range bombardment ships it's pretty good with, but it has no idea when it should charge in or stay back with e.g. a 3x Antimatter Blaster Shade or a melee Enforcer. SO is for player piloted ships only, I find.
The increased OP needs to stay in one form or another, whether it gets built into the ship or blueprint or whatever. When I go back to play the missions, I can't believe how restricted the builds you can make are. Very high OP weapons, like Tachyon Lances, Light Needlers, etc. would just never see play if you didn't have the extra OP.