Sid Meier also said that "given the opportunity, players will optimize the fun out of a game", which is what I think you've done here.
Frankly, I'm impressed that you found this "exploit", I wouldn't be surprised if you're the only player to ever do it- I'd never thought of using support doctrine like this till reading the thread.
And this brings me to the second half of the quote I mentioned - "one of the responsibilities of designers is to protect the player from themselves."
I broadly agree with FooF & BCS; there is no problem to fix here, you can either just not care (because seriously, 4.9333...% extra damage is meaningless) or achieve the same result through different means (crew training, combat endurance, hull restoration + smods, etc), you've just found a perticularly tedious way to get there.
any changes to any of the mechanics here would be meaningless, at worst they'd be getting rid of an interesting strategy- using an officer to get the +ammo from missile spec without taking the skill yourself, you have to decide if that boost is worth losing out on an extra officered ship - & at best they'd be so carefully specific that they'd be fixing exactly one "problem" that (as far as I know) only one person has ever encountered.
and don't even get me started on "playing optimally" - arguably there is no such thing as optimal play in starsector because there's no set end goal.
though I do agree with you on the mission side of things, a few types of missions (particularly spysat deployments) are just permanent no-takes for me because they're basically always targeting planets that are a PITA to get to undetected; they deserve a looking at.
... but I don't think that your solutions actually offer any interesting decisions (for the mission and skills), they mostly just add extra steps to things that are already doable.