Holy poop will you stop talking rubbish. Speaking as an actual engineer who's worked on specialist automotive projects for the past 20 years I can categorically state that you don't have the first clue what you're talking. The degree of RNG is WAY beyond anything that can be attributed to "tolerance", so stop trying so hard.
Taking to one side the fact that in-game your hanger can 3d print a fighter from scratch in a minute (which would suggest that the engineers, being at the pinnacle of the tech curve shoudn't be using any old rubbish you bring them, but rather melt them down for the raw materials to go into the 3D printers. Failing that they could, you know TEST them to make sure they're not putting rubbish in there), by your argument Rank 1 Upgrades *should* have very little RNG, after all, they're only Rank 1. Rank 5 is "bleeding edge", so Rank 1 which offers considerably less improvement is, what? "A-bit-sore edge", Rank 2 being "slightly-bruised edge?"
It's a lazy mechanic, that's never proven to be particularly popular and appears to be breaking the game - cue the month long combat beta for rebalancing.
All they need to do is get rid of the Weapon special effects. If they do that, then all this becomes manageable. Until they do however, space magic will be king of the day when it comes to combat.