For me, the most attractive feature of Safety Procedures is the lowered threshold for malfunctions. It is like a reverse Fleet Logistics 3. Not as good, but it extends the time ships can fight before breaking down. Of course, once malfunctions start in battle, you have even less time to retreat your ships before CR is too low and they cannot move anymore. Of course, if I get 2 for that perk, might as well get 3 for less punishing (D) mods and free EB.
Because I always get max Colony Management and Industrial Planning (because I do not use cores), Safety Procedures would only cost me two or three points. Of course, it is not that simple because I am already just one to three points shy of getting everything I want even if I ignore Safety Procedures. Thus, Navigation or one other QoL skill is on the chopping block, and it kind of hurts. I could give up a combat skill, but then I would be noticeably weaker than my officers. I would have enough points if I abused alpha cores and ignored Industry altogether, but I like personally governing a sizable, self-sufficient empire, and I do not want to resort to or rely on cores to do that.
As for pristines vs. clunkers, I probably made it to endgame in my current game, and I have not yet found enough blueprints and accumulated enough money to replace my clunkers with pristine ships. Being able to mitigate (D) mods would be very useful until the very end, much like Colony Management 1 before a core user finds enough alpha cores to abuse.
Yes, it is annoying that I need to give up quality of life, especially Navigation or any colony skill not named Fleet Logistics, just to have a better combat flagship and/or fleet. It would be nice if combat competed with combat, and QoL competed with QoL, not this weird mix where you give up QoL just to be good at combat.
At first, I thought level 50 gave enough points to overcome the twelve dead aptitudes, but now that most major lore NPCs (that were not in the campaign in 0.9a) have 3/3/3 colony skills like alpha cores, and they probably were level 20 officers when they commanded fleets instead of colonies during their prime, I do not think we have enough skill points to match those lore NPCs. Given the current skills, I probably get 3/3/3 colony skills if I give up combat ability (only about level 15-17 instead 19 like my officers, sort of).