Let me link you to two items from the Macross Mecha Manual website that should clear up why the VB-6 can't fire it's rail guns while in shuttle mode. I suppose you could, in theory, but by the time you get the big guns out, you're mostly in GERWALK anyways.
http://www.new-un-spacy.com/macrossg...iordetails.gif
http://www.new-un-spacy.com/macrossg...formation1.gif
Amusingly, the parts of the guns that point backward can be used to generate more thrust in shuttle mode, but to swing them forward and fire would not be good in space unless you wanted to decrease your forward thrust. Macross at least pays lipservice to realistic physics and screwing with your forward velocity in the middle of space combat is a bad thing.