I have no opinion as to who created that hole in the door of the presidential box, but I always try to find the simplest answer. That being said, one thing that would have a bearing on whether the hole was pre-Booth is whether any of the other box doors at Ford's had similar holes in them.
Am I correct in my thinking that at least three other boxes at Ford's--one underneath the president's box and two opposite--would have had similar doors? If any of those doors had holes, then that would decrease the likelihood of Booth having bored the hole in the presidential box's door.