Yes, the transmission would not move enough to make contact with the body, but it could easily be moving enough to change the driveshaft angle enough to cause a vibration.

What happens with the u-joint is that it changes angle only a microscopic amount. This causes the u-joint to wear in a very close area. If you were to take out the driveshaft and flex the u-joint, you very likely would find each axis of the u-joint stiff with the driveshaft straight, but smooth once flexed beyond that point. By changing the trans mount, you may very well put the driveshaft into an angle that will not vibrate even when hitting a bump since the new mount would not flex downwards near as much.

If the trans mount does not cure the problem, you may need to put a few washers between one side of the carrier bearing mount and the body to put the u-joint in a slightly different area, away from the worn spot.

Good luck,