The problem is that even the non-Duo blocks the second PCIe slot. Having 1 full length slot with the MPX slot changes the dynamics a lot, considering you can’t use either of the Promise internal bays, and will be more reliant on external I/O vs the Pro and only 4 rear ports vs the iMac.
the "half width" MPX module doesn't block the slot if just want bus power. A MPX bay consists of two double wide PCI slots.
"
Each MPX bay provides:
.....
Alternatively, each MPX bay can support:
One full-length, double-wide x16 gen 3 slot and one full-length, double-wide x8 gen 3 slot (MPX bay 1)
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https://www.apple.com/mac-pro/specs/
Each MPX bay has three sockets. Two PCI-e ones and one "MPX connector". There is a double wide gap between the PCI-e ones. The two MPX bays cover four double wide slots.
So yes the single Vega II soaks up lots of space and if coupled with a the Promise MPX storage module then have two major slot coverers. I extremely doubt though that is the configuration that Apple is thinking most will go with. Folks with big budgets will get a Duo and storage MPX and be done.
Also, the J2i does absolutely nothing to slot capacity at all. It is in a different zone of the system (CPU zone, not the slot zone). If the next gen HDD density tech trickles down to 2.5" drive then a future 'cousin' of the J2 could pack four 2.5" drives up in that zone. There is probably a future path there for folks who 'love' HDDs and don't need contemporary fast storage.
Apple didn't optimize this system at all for HDDs. The more HDDs stuffed into the internals the more "problems" will pop up.
Pushing folks to non-Apple GPUs if they need more I/O is a weird statement for Apple to make,
But they aren't pushing folks. At least those with money/budget. If Apple goes back into Rip Van Winkle slumber then perhaps that would be a "push". However, if they just do a few things there isn't much there.
One, replace the 580X card with something better in 6 months or less. It is pretty apparent that card is a bit of a fluke of timing rather than their desired objective. If Apple's entry base card was a RX 5700 based card they'd be less of a need for third party stuff. Same issue 12-14 months if iterate on the Vega II cards.
Two, expand out robust support on add in cards for SSDs. "more I/O" isn't really where HDDs fit in. Relatively it is much less I/O to keep a HDD pipe filled than a SSD one. HDDs have more capacity.
considering the effort made to keep Thunderbolt 3 relevant for display output in the Mac Pro.
DisplayPort 2.0 is built on the Thunderbolt protocol. The number of GPU cards with "Thunderbolt" is only going up in 2021 and later. The notion that Thunderbolt is going to drop of relevancy ine upcoming years is odd when it has been weaved into USB4 and DP v2. It isn't going anywhere. And Apple isn't the only one that is going to be keeping it relevant.
The third thing Apple can do is not be quite so proprietary when DP v2.0 rolls out and more folks may be interested in dual usage output on new generation cards. ( i.e., work with some folks on using MPX connector as a pseudo standard).
You cut out the important bit when you quoted: the Thunderbolt card. Gigabyte produces two (Alpine Ridge and Titan Ridge) variants that include dual DisplayPort inputs. Can’t do it without that, I agree.
Apple isn't going to spend much time putting support in for 3rd party legacy TBv3 cards. The Titan Ridge ones can be put into a "happen to work" state but Apple probably won't spend any more time on that than they do with eGPU on the MP 2013.
Rube Goldberg, external 'loop back" cables. Apple isn't pushing people to that. First, there are tons of folks sitting on older displays that don't have Thunderbolt. They will be happy as pigs in mud with a 3rd party GPU card that is supported with official drivers in the new Mac Pro. For the XDR .... if can afford it then probably can afford Apple's GPUs. The Apple constrained LG Ultrafine have one, and only one, input, but most other monitors that have TB input have more than one input. Those 3rd party monitors will work with 3rd party GPU cards.
There is only relatively a narrow corner case here where there is a mismatch. Most Mac Pro users don't have Apple "one input" monitors. That isn't going to change with the new Mac Pro.