I agree that if the shell plate is misaligned at the time of primer seating, the primer plunger may be pushing against the brass instead of only the primer. And that will definitely prevent the primer from seating properly. It's a lot easier to check primer shell plate alignment that you described. Just take 5 empty unprimed brass and rotate it thru the stations without any primer loaded into the press. Go thru the motion of priming. If when the brass is at the primer station and it moves left or right or rocks back and forth when you try to prime, it is not aligned properly. Often times you will find the brass move towards the center of the shell plate slightly. That is fine. The movement is the plunger entering into the primer pocket and aligning the brass. This also proves the plunger can and will go deeper than flush when seating primer. Which leads back to shell plate deflection as the next culprit in not being able to seat primers properly.