I doubt you'll notice any issues, as long as you mount the trackball with it's "top" facing the backside of the box.
You might have to get used to the angle, but that shouldn't be a big deal.
The thing to watch for is mounting the trackball such that the monitor is very close behind it. Given many trackball games require you to really smack the ball, you could end up smacking the backglass and monitor. But that won't have any effect on the way the trackball works, just your hand
