Again, you have made a great observation.combine that with the potential massive hull HP inflation and FD have an impossible task making that lot playable but challenging for everyone.
Memory tells me that NPCs had to be tailored for the baseline player (so unengineered) in anything but CZ and 'special case' Pirate massacre missions.
I've taken unengineered ships into a Haz Res and survived, but not exaclty excelled in massacring many

My All Multi (G5 everything that matters) FDL can take out all 4 Spec Ops in a CZ without too much effort - but only if it can take them on 1 at a time!
I'm not one for 'meta' builds, I try to not fly a God ship and then whine about how there is no risk, even my best combat ship can (and has) be forced out to lick its wounds, it does make for a great experience, for me. (Others would be very derogatory about the builds as they are too weak, so are 'bad' builds)