Constrained design
If you're wondering why there are two GPUs in the Mac Tube Pro, the answer is it's a required design constraint. The constraint follows a sequence of design decisions.
Apple wanted to eliminate internal PCIe slots, and use Thunderbolt instead. They didn't want to have special data-only Thunderbolt ports, so all Thunderbolt ports need to support displays. Without PCIe slots, 4 Thunderbolt ports would be too few, so 6 was chosen as the minimum.
The resulting architecture is a single Xeon CPU and two FirePro GPUs. The FirePro GPUs support what AMD calls eyefinity, which simply means it can route the display channels to different connectors as needed, and support multiple displays simultaneously.
The Mac Tube Pro has 7 (including the HDMI port) possible display connections. According to Apple, three support dual-link equivalent (over 1920x1200 pixel) displays. This puts a floor on which FirePro GPUs can be used.
The PCIe architecture therefore is like this:
1 Xeon CPU
32 PCIe lanes to the two GPUs
24 PCIe lanes to intel Falcon Ridge controllers, which join 6 displayport channels from the two GPUs, out to the 6 Thunderbolt ports
4? PCIe lanes to the internal SSD slots
1 PCIE lane for internal platform controller
