When I mount them in Golden Tee's I take the plate, route down about 1/16+  until it's flush.  I take a drill and put in the mounting holes for the track ball plate. 
After that, I rough drill with a 1" or better spade drill.  I take a jigsaw and cut out a big hole for the track ball all the way through.  It doesn't have to be pretty, it's just clearance.  
Then I put on the mounting plate. Then I usually don't fill around it (with wood putty or anything.  I cover the plate with a CP overlay.  Shelf paper, mylar, or whatever.  I then take a piece of plexi and a drimmel tool with a cutter and a drum sander and cut out around it. 
Using the holes in the cp a guide, I bolt the plexi on the cp and rough drill the button holes and the plate.  Then I cut the holes to size with the drimmel cutter and drum sander.  If the plexi is thick around the track ball, I cut a chamfer (bevel) 360