Finefinefine...
The carriers in WC3 and 4 have catapults... (the Victory has one, the 'Lex has two). You can fly around inside the bays because the engine designers were fly-around-inside-stuff crazy... but when you autopilot out of the ship, that's you being catapulted into space.
The reference to two bays in the Concordia class ships is that there are two repair/arming/etc bays, one on each side of the ship (to support each catapult). THus, the Black Lance stuff was housed in one bay on 'Lex, and the regular wing in the other.