Hi Joe,
When I had Fuji AF lenses, I used the intermediate size, and just made sure I was pointing it in the right direction. 🙂 I don't remember ever having a picture turn out to be focused on something other than the intended. Maybe there are certain types of photography that are more conducive to using small, medium, or large boxes? That would be an interesting line of inquiry here. For example, for slow, purposeful landscape photography maybe the small square would make it easier to focus on one tree rather than another. And maybe the same applies to portraits where DOF is tight and you're trying to stay focused on the eye closest to the camera?
Anyway, now that I only have manual focus lenses on the X-Pro1, I'm quite used to using the magnification tool or zone focusing, depending on required speed.