That's a fair point, but I think FD have very deliberately gone in this direction.
They don't want the upgrades to be done in a deterministic fashion. If there is a given path to (say) a weapon that deals the most DPS, then that's what the vast majority of people will take. Regardless of how much it costs, or how long it'll take, or the effort involved. Because no one wants to feel at a disadvantage.
If so, the net result of Engineers will be everyone spending a lot of time just to end up with the same set of upgrades as everyone else. To me at least, it seems the goal of Engineers is to provide variety, and such a deterministic approach would add none. With the current approach, even if several Cmdrs all opt for the same upgrades and re-roll to optimise the same stat, they still will never end up with exactly the same modules, they'll always be marginally different.
As it stands, crafting is a choice-based rather than skill-based process. It's about customising/optimising your ship to your playstyle, rather than using your experience/sills to improve your ship more thus increasing your advantage over less skilled/experienced players. I can't speak for everyone, but personally I'm fine with that.
From a realism perspective, it works well enough too. In engineering there's not really such a thing as equality, everything is within tolerances. In Engineers, the tolerances are exaggerated because they have to be. If the tolerances were <1%, we'd be back on the deterministic path that FD seem to want to avoid.
If they didn't want players going to upgrade what they want to upgrade then they shouldn't have introduced engineers to begin with. That is nothing more than an excuse. If they were so worried about everyone having the same thing then they should have made buying the modules an RNG roulette instead. At least then everyone would know that they have no control and no say over what they get.
And no, as it stands, it is NOT a choice based system and it is NOT about customization or optimization because by the very definition and nature of RNG both of those are literally IMPOSSIBLE. And neither is it at all realistic, how many times do we need to state that engineering is an actual science and not a gamble in real life? You don't go to upgrade your motor and get a bloody loaf of bread like we do with this update! Again, the exaggerated tolerances are not needed and no, they don't have to be.
This whole system with the engineers is nothing more than a cop out, or, the worst possible game design ideological standpoint. This is stating exactly this: "Lets implement a system that gives the illusion of choice and customization but actually takes all control away from the player just to make them waste more resources."
Until this sorry pile of weakness is changed into something even close to resembling a system that allows choice/customization/crafting there are going to be a great deal of unhappy players and casinos that sit idle.