I can't really remember that particular scenario happening, but I haven't played Prophecy in ages. Manual launching is a hectic job, especially if you only have a bay that runs the length of the ship, since any fighter leaving needed the necessary velocity, independent of the carrier, long enough to move out of the way of the carrier it just left. (It seems contradictory to Newton's First Law of Motion, but I recall that, at least in the WC4 novel, it being made a big deal of. SciFi Physics, go fig...) The Midway could have, of course, simply "pushed" fighters out of the rear landing bays, but it would be a time-consuming process, taking a long time to launch a squadron.
And I don't know which "older carriers" you're referring to.