Yes, the carrier bay would ignore logistics and the hyperspace speed of the embarked ships. That way you'd have actual 'fighters' that would use the carrier as thier primary means of mobility. I think it's a pretty good method, but it really doesn't matter unless the devs agree too

At the same time you don't really need 'fighters' unless you create a much more involved combat system from what it currently is. That isn't nixing the current combat system, I quite like it. But to really have a use for 'fighters' and 'carriers', you'd need things like manuverability, rate of fire, even ranges for weapons to make fighters and carriers neccessary or relevant. In the current combat system, they simply aren't needed.
My biggest gripe about the combat system is that it is flat: mass drivers are the same as beams are the same as missiles. Missiles don't have a longer range, and beams and drivers don't have a shorter one. This puts combat to math equation of how much more stuff I can fire, and can I fire stuff you can't defend against. This isn't bad, just a bit...flat.
Ok, and as to the actual topic at hand:
I've got a 'tiny' troop ship that mounts a single Adv. Troop module, a 'tiny' constructor, and other such things. I find they make nice, cheap ships for doing stuff that I don't need a full transport with engines or a more expensive constructor with life support, engines, etc. This is especially applicable when I'm building a network of starbases close to my planets. The tiny troopships are great for assaulting neighboring planets--the ones that are only 1 or 2pc away from one of my planets (happens alot with everything set to abundant).
Tinys have thier place for sure. But relegating them to a combat role may be where you're coming up short. Think of other stuff you can do with them, maybe just a fast sensor ship you can fleet with stronger ships so now you've got cheap and disposible sensors without taking up that space on your main combat ships.
Hmm...that's a good idea. I think I might have to try that one myself