I have "In the beginning" too ! Very touching movie.
Anyway,as far as I know, first Omegas were built after the war, I don't think Earth would have started to build a whole new ship class during a desperate war, they lacked X-Ray beams and all....
Whitch bring me to Nova-X. What it had so special to be called "X-class". I mean were they some kind of prototype Omegas.
As for those transports/carriers/Shuttles seen during the Epiphanies, they didn't seem to have any external weapon pods or cannons when they carried those Black-Omegas. For me they seemed to completely unmodified and completely unarmed, only larger. Though they might have some gunports, which would convienently hide those weapons.
I could post a few small screenshots, but there's one slight problem, I actually have never posted any screenies before, could someone be kind and give some...instructions.
I know it should be very simple process, but one does not know until he asks.