Haha, no way man. There is no way this mechanic could actually make real sense. It's just for gameplay. Trying to justify it is a bit of a hand wave.
For example, I buy 500 supplies from the hegemony and go blow up some tritach fighters. I get a wasp wing, then engage a carrier fleet with them. They resupply 2 times in that fight. Did I just buy wasps from the hegemony? So obviously that doesn't make sense. Carriers are the same because that's easier.
In that example you got some supplies when defeating the first Tri-Tachyon fleet, so replacement fighters could be in there. Well, it's not perfect, but it's something.
I still would like to see it changed, but now mostly for gameplay reasons.
I feel like this is adding needless complexity. What about the other stats that already differentiate them is lacking?
The condor and gemini are VERY different in terms of how and where they can do their refitting This affects how long it takes to repair since fighters have to fly all the way back to your condor on the back lines when your gemini is usually in the thick of it.
Also there's the consideration or their rarity in the campaign and the difference they will have on your fleet economy.
Mh... the Condor has better hull and two times the armor of the Gemini, which in turn has better shields. They are both not qualified to stay very close to the front lines, I think.
But honestly, the Condor is transformed into a dedicated carrier, giving up almost all storage room. The Gemini is a heavily armed transporter that happens to have a tiny flight deck. And the Gemini is just as good (or even better according to you) in a pure carrier-role as the Condor (or the Venture or the Odyssey)? That doesn't make sense to me.
