I agree that option 1 may put the AI at a disadvantage if the human always chooses the mass bonus options in order to build "Super Carriers" the same way I tend to build super constructors . Option 2 seems to avoid that.
One note, in my last game the Federation AI made use of carriers consistently, by the later part of the game dreadnoughts and carriers are all it was sending at me. if it had been capable of using its logistic points competently I would have been in real trouble. Not sure if any of these options would affect this tactic.
I do agree that the way carriers are represented in the game is more reminiscent of Battlestar Galactica than Star Trek, however, some versions of the Negh'Var in ST canon can carry a bird of prey, Option two would seem to be more closely associated with this. On the other hand, the expanded universe has carriers and the Dominion even has super-carriers. http://memory-beta.wikia.com/wiki/Category:Carrier_classes