I was thinking of the complications and apparently not communicating well. I meant that the actual CG of the as assembled vehicle doesn't change throughout the flight, but weight on the mounting points that the original aircraft experiences changes with airspeed.
I'm not an S&C guy, so it seems complicated to me, but I guess if you consider it as one vehicle (albeit a very oddly shaped one) you can work out the stability derivatives just like anything else. But being a tester, I'd probably just head to the wind tunnel.