I think you're right Jose, the same rig on a different mount isolates the one variable we're interested in; you'll prove the performance of the kit and that will just leave the mount. I think this exercise will produce valuable evidence.
As you identified, perform the trial in the same area of sky where you had the problem.
It might be worth doing the guiding assitant trial before switching to the other mount, just so you're testing the current context before making any change. Then change to the other mount and repeat.