Flight decks are a bit common in non combat ships
They're really not. The Atlas is the only noncombatant that has a flight deck, unless you consider both the Condor and the Gemini to be noncombatants (despite the Gemini's claim that it's a freighter, it's at least as much an escort carrier or light carrier as the Condor and not nearly as much a freighter as the Mule).
As far as the fighter officers as fighter aces idea goes, I'm not terribly fond of that idea. I don't really like the thought of having this guy somehow teleporting from a fighter that just blew up into another fighter or a carrier that started building a replacement fighter; officers should be out of action if the ship they're on blows up, and that includes fighters if they're supposed to piloting one personally. I also don't like the idea that I'd have one superfighter per squadron with the rest of the group performing at the current level.
As far as the idea of tying fighter performance to carrier commanders, I'm not terribly fond of it. I'd tend to prefer that fighter wings had their own officers, rather than being the one unit type that depends on some other character for their performance. That being said, there could be skills for carrier commanders that indirectly affected fighters, say skills which boost the speed at which flight decks rearm, repair, or ready fighters (which would tend to be a carrier crew thing rather than a fighter thing). Direct performance enhancements, though, are something I'd much rather came from an officer assigned to the individual squadrons.
However, I could see tying the number of fighter officers you can have to the number and type of carriers you have. I don't like the officers as fighter aces idea, but that leaves the question of where fighter officers would go and what they'd do; putting them into the carrier seems reasonable since you'd expect the carrier to have something like an ATC, the size of which would likely be at least partially dependent upon the number of flight decks on the carrier (though you could have a nonlinear scaling, e.g. a Venture or an Odyssey might have a larger ATC than a Condor despite both vessels having only one flight deck), and keeping them in the carrier to staff the ATC explains what they're doing if they're not fighter aces.