I think maybe I'm confusing you. Forgive for the crappy pic but....
http://oi59.tinypic.com/nqcnc5.jpg
There I have the pin assembly clamped in a vise and the bolthead just set on top of it with protrusion set to .03455" (.035") from the boltface to the tip of the pin or what I call the "bench" protrusion setting. When checking an as-is or a re-profiled pin tip I use the same setup but set the protrusion to .020". That way I can see how much or little clearance there is between the tip and pin hole.
If you look back at the pics of the pins-bothhead I posted earlier its what I'm looking for, the amount of clearance between the two pins. I haven't found a way to accurately check the amount clearance so I just get a close length measurement from the tip of the pin to it's shank. If that length is .020" or less I assume the full diameter of shank is in the pin hole when the pin strikes a primer.
Clear as mud?:p
Bill