The lower zone earns my admiration, bordering on awe. Heatsink-mounted fans always struck me as a horrible design. Yes, they sit right on top of the thing that wants cooling, but the airflow is haphazard. In most of the designs with which I'm familiar, the airflow is poorest at the center where the CPU needs it most. Apple's approach is atypical. Mac Pro's heat sinks rise high above the motherboard; I believe they're on risers, but again, without permission from Steve, I won't break open this loaner to find out. Memory sits several inches from the CPUs, and memory (and support components) sits on a pair of removable riser cards that, like the PCI Express expansion cards, stand perpendicular to the motherboard. One strong fan pushes air straight through this alley while the single fan at the rear sucks it out. And of course, you've got the whole chassis acting as a heat sink.
Cooling is a big deal in Macs because Apple will not throttle its CPUs down until they reach critical temperature levels. I have tried many times to push Mac notebooks and desktops into thermal shutdown, but I've never been able to do it. A MacBook Pro in "better performance" mode will (do not try this at home!) ran for several hours wrapped in a comforter. It was practically glowing hot when I unwrapped it, but the benchmarks I had left running showed that the CPU never throttled down. I got confirmation from Apple that this is consistent in Apple designs. To put a twist on Phoenix weather reports, "Macs get hot, but it's a quiet heat." I haven't yet taken Mac Pro down to my 108 degree garage to run sixteen simultaneous SPECcpu processes. That sounds like a weekend thing.
Oddities: I found a number of empty pads for small to moderate pin count surface-mount ICs on the motherboard real estate visible in the expansion card area. I'd rather imagine that these are reserved for some nifty future features than believe that they're just leftovers from scotched portions of earlier designs.