I thought that the ARMD carriers were destroyed, and it was the (semisubmersible) aircraft carrier Prometheus and the (semisubmersible) BIG landing craft Daedalus that were attached to the arms ... (Which allowed the "Daedalus" attack - put all the barriers on the front of the Daedalus, "punch" through the enemy craft, open the door, and have the whole crapload of destroids behind the door destroy the ship from the inside.)
Might just be a difference between the movie, which I haven't seen, and the series, which I have ...
To go back on topic, the VFs were mainly stored on the Macross. Only a few were on the Prometheus ... however, (in the series) it always looked cooler to launch them from an aircraft carrier, so that's the clip they always used (esp. for Lt. Ichijo ...)
I like that this mod is back to working status!