This is what I plan on doing. However, recently I read that you need to Bondo out the surface of the CP (OVER the mount) before you put the adhesive CPO on and the plexi on top. Otherwise you'll see every bump or pebble grain from the mounting plate....
That's possible if you have the black powder finished plate. The "clear zinc" won't (except maybe around the edges). Also, it depends on the thickness and material of the overlay. A thin overlay will clearly show the powder finish, but a hard, thick overlay might not.
...But then again, if you put the mount deeper into the control panel, where would the lip of the trackball lay in relation to your plexi? I imagine that ideally you would want the lip over the top of your plexi...
I'd want the top of the lip to be
exactly level with the top surface of the CP, the top of the plexi in this case. I've seen the lip sticking higher that the surface; IMO it's ugly and the lip is in the way of the ball so if you run your hand along the surface, it will hit the lip instead of the ball.
The high lip TB models has a 3/16" lip, which is perfect for the 1/16" mounting plate + a 1/8" plexi, or directly under 3/16" plexi. Overlays are usually thin enough (1/64"-1/32") to not make a noticeable difference. But over 1/32" is too much IMO, and it's easier to fix a protruding lip (four plastic spacer washers) than a recessed lip (thinner plexi or route round edge plexi). So be careful how deep you route the plate.