No the trackball stays in when it's upside down. More than half of it is below the top of the case. I don't know about the high ones.
FWIW, ~0.6" on the normal & highlip 3" (or 1/5th or ball diameter), ~1" on the high ball (or 1/3rd), for the happs TBs. Betson & wico are very close, if not the same, as the normal happs as far as amount of ball above top.
edit:
BTW, since this is for a rotating CP, it might be a good idea to open up your TB before mounting it, and look for any extra plastic, um, "flakes" left over from casting that should have bin sanded off. Usually they are taken care of, but one small extra one scratched one of my balls when I turned the TB & ball over.

The "lip" the ball will rest should be smooth out of the box, so look at the surounding structure reenforcements.