Scott,
This sounds like it might become a "pissing contest" between you and the DMV in Mass.
I have never heard of a state not passing(other than noise restrictions) a vehicle because it had a modified exhaust system. As long as the VX passes emission standards there should be no questions.
(Otherwise buy an acre in Vermont where we don't have those problems..JK)

I would make a phone call to the Commissioner of Motor Vehicles and get the real scoop on what's going to happen now before it gets nasty.
John