I believe Apple has added a proprietary interface to this slot that routes DisplayPort video.
Probably GPIO also. Since it probably can handle live plug and play events and Thunderbolt network reconfiguration events ( unlike the hacks on the MP 5,1 ).
This is what enables the TB3 ports to display the video from MPX cards. Because it requires this proprietary interface the card can not work in other slots (or older Mac Pros).
I think they may have used the PCI-e pins for something other than PCI-e . IF you plug it into a regular PCI-e slot that slot will take those for PCI-e and at best quirky things would happen. If Apple went down that path then the prudent thing to do is set up the card firmware to just 'quit' if senses someone plugged it into the wrong slot.
Better thing would have some physical notch displacement so just can't plug it in 'properly'. There are enough hackery card options out there that Apple doesn't need to pile this card on top. But I think they wanted the option to put standard PCI-e x4 cards in there so I don't think there is a physical block for that. ( possibly opens door for bad things if someone tries to put in some bigger than x4 in there. ).
I think it is removable because some folks blow out USB sockets ( and maybe some Thunderbolt sockets ) with cheesy implemented power options plugged in. If you blow out a socket then it is a simple board replacement.
There also may be a "certified USB4" option coming later too. Won't need any more bandwidth feeds than what they have now. I suspect that is a bigger driver (especially if they plan to disappear for 2-3+ years again ) .