I wouldn't say it's so much an abuse of the rules if it happens so much as it would be abuse of an overly permissive GM. That's one of those cases where you have to step in and enforce the spirit of the rules rather than the written letter.
The problem IMO is not with the Flip Belt but with the Pilot skill. What does piloting something that's several km long and takes 30 min to turn 45 deg has to do with agility?
So much this. The Operate/Pilot skills in WH40kRP have always tended towards being a ***********. Worst is that there's no reason for it to be that way.
Piloting a large Voidship should clearly be either Intelligence or Fellowship, depending on the ship and the manner you control it.