As an IT manager dealing with many many Wintel towers I can tell you this, placing them on the floor is the fastest way to kill a computer. That being said, since the Mac Pro's CPU does not have a fan on it to seize up from dust, it may be less of an issue, it depends on the fins of the the heatsink. Even so, the fans are much more likely to start getting noisy and eventually seize at a much higher rate than if it was off the floor.
After seeing the countless damaged computers (from inhaled dust) that were sitting on floors, I'll never let one sit under my desk ever again.
But what if you open it monthly or every two months and air spray it out? will that harm it?