Not all Thunderbolt 3 ports are the same. Good chance that two ports are sharing a single PCIe 3.0 4x controller. Since PCIe 3.0 is good for ~7.8Gb/sec/lane, you're looking at two 40Gb/sec Thunderbolt ports sharing about 31Gb/sec of bandwidth on the PCIe bus. Okay, probably not that big of a deal really.
The point being that a "Pro" system might have 4 individual Thunderbolt controllers, each getting their own 4x PCIe 3.0 lanes.
I think that's why the specs say "Up to 40GB/sec" on the page. It sadly doesn't say which controller it has... But I guess my whole point is really moot in practicality. Good luck saturating that much bandwidth.
Mac mini, iMac Pro, and Macbook Pro all have two Thunderbolt 3 controllers.
The Mac Pro starts with two controllers but can be configured up to six.
The I/O is actually pretty good and provides for a ton of headroom for expansion down the line (I'm thinking primarily storage and GPU for my use-case).
I can see a pretty high powered eGPU saturating the lanes.
The point being that a "Pro" system might have 4 individual Thunderbolt controllers, each getting their own 4x PCIe 3.0 lanes.
I think that's why the specs say "Up to 40GB/sec" on the page. It sadly doesn't say which controller it has... But I guess my whole point is really moot in practicality. Good luck saturating that much bandwidth.