I don't think the point was that it couldn't refuel with a gunpod mounted, just that they would not eject the gunpod for Roy to catch while it was being fueled.
At this point in time Roy is one of the few who can really handle a variable fighter with experience. Having a pilot switch to Gerwalk and catch something while taking on fuel while being something Roy might be able to pull off, would be a pretty risky move for most other pilots, hence being against regulations.