I look at it this way, Apple says don't do it, they designed the thing, they must have their reasons.
Although if you hired your own engineer and found out you can with some PowerMacs doesn't mean everyone can with all PowerMacs.
So unless you hire your own engineer and take the responsibility on yourself for the repair costs associated with not following Apple's guidelines, then it's best to do as they say.
For example, the University of Virginia Tech built a supercomputer of 1100 DP PowerMac G5's and everyone of them was upright. (they now use the X-servers)
Another example, a video rendering outfit near Hollywood has over 600 DP PowerMac G5's as their render farm. Every one one those in their render room is upright on large metal shelves, instead of laying on their sides in a labor saving rack mounted system.
So until Apple says somewhere that certain models of PowerMacs can be safely on their side, I wouldn't do it. The damage may occur slowly and not appear until after your AppleCare has expired.