Oh snap. I don’t mind losing the video from the top and rear ports. I thought I was going to lose the Thunderbolt as well.Yes you will lose Thunderbolt VIDEO from the top and rear IO cards, but not regular Thunderbolt for data. Only MPX GPUs support Thunderbolt video from all ports if it's in the machine. The Intel 7,1 Mac Pro routes GPU video properly through all Thunderbolt ports if there is a MPX GPU in the machine. If there's no MPX GPU in there, Thunderbolt video is ignored on all ports.
Thunderbolt also supports USB-C DP Alt Mode which means that you can connect Thunderbolt monitors into a GPU that has a DisplayPort. The USBC port on the 6900XT also supports DP Alt Mode, but it will be for video only.
I had the 580X MPX and pulled that out a long time ago since it's a very slow GPU and for dual 5K monitors its not enough. I now just run the 6900XT to Apple Cinema Display 5k (dual) with no issues for years using that cable I provided a link to.
It is a known issue that if you have a MPX GPU and for example a 6900XT, the OS doesn't know exactly how to switch it around and to use what. You don't need to have the MPX GPU in your system at all, it's a waste of a slot + performance drop.
What monitor are you using btw?
I think I am going to run with the W5700X for a bit just to confirm everything is happy. I want to upgrade my USB PCIe card so I think I will order that and then swap both at the same time.
Running three U3225QE. Upgraded from three U3015 that were starting to show their age. I can’t get over how much extra space I have on my screen going 4k.