If that assumption isn't correct all cuts with the base as a reference will be wrong.
Another way of checking for 90 degrees is to make a mortice in two boards. Insert a tenon into one of the mortices and flip the boards over onto a flat surface. The face that the fence referenced should be down. Apply some downward pressure to assure the boards are flat and bring the boards together. If the mortice goes into the emtpy mortice then your at 90 deg. This techique doubles any error. I think I got this description correct. This works for checking a biscuit joiner too.
I'm unclear how what you described doubles any error. If the fence is off registration on both boards, I think the test would be fine even though the fence was off. Maybe I just didnt understand your description.