I'm not sure what you mean by less clearance inside the CP box. If you mean it doesn't sit as deep, than yes, but we're only talking about a tenth of an inch. Basically with the highball, the ball just sits up higher out of the trackball case. So yes there is a little more ball to play with. The highball actually does use a different mounting plate than the regular. If you don't want the mounting plate to show up, just route a recess for the mouting plate in the CP, then cover it with your artwork. Trying to mount the trackball from the underside of the CP and have the ball come through a circular cutout in the CP is not going to work to well, you'd have to route a very deep recess with isn't going to leave you with a lot of strength. I'm sure it can be done, but not really the best way to go about it.
Ideally the best way to go since you're using lexan is to get the "high lip" otherwise known as Golden tee trackball. Its meant to be mounted under 1/8" lexan and so it allows for that and allows the trackball to sit at the correct height even through the lexan. To get the flush trackball look minus the mounting plate, route about a 1/8" recess in the top of the CP to mount the trackball mounting plate flush. Then cover with your artwork. With the high lip trackball, this leaves you 1/8" of lip from the trackball case sticking up. This is to compensate for the 1/8" lexan you would then be adding.
-Kevin