I hear what you’re saying, but it’s not 2006, it’s 2019, and apple should realize that folks are going to be putting high end 3rd party cards in their top of the line machine. I’m not disagreeing with you, in the sense that it seems that the design of the Mac Pro was based on these older assumptions, but I assume ASUS and NVidia and AMD were all designing 3-wide cards at the same time as the Mac Pro was being developed.
For the Workstation and Server market? Generally there were not doing 3-wide cards.
Nvidia has a semicustom workstation box with 4 cards in it. They are all double width and water cooled. The water cooling allows them to ballon squeeze the extra bulk required to another part of the enclosure ( the top to blow it up and out).
ASUS just introduced a new ATX motherborard for creatives.
Every aspect of ProArt Series motherboards is built to remove barriers and deliver optimal performance to content creators who work in 3D modeling and rendering, animation or media production. The series empowers you to concentrate on your creativity and expand what is possible.
www.asus.com
3 wide spacing there for non slot blocking? Nope.
Standards like ATX and EATX are also fixed in size. If given a fixed amount of space if the board maker tries to increase the space between slots then will likely have to trade something off. (e.g., give up a slot ). Slot numbers sell on most enthusiasts groups more than "better spacing".
The biggest Dell box 7920
The block of 3 slots on the top provisioned by the second CPU. Two x16 there but if stick in a 2.5-3 wide card blow away the other x16 slot. Similar issue on the bottom if put in a 2.5-3 wide card. You have just lost space for two more x16 SSD cards and a Declink card.
HP Z8 description:
"... Up to 2x NVIDIA RTX™ A6000 or 1x AMD Radeon™ Pro WX9100 "
https://www.hp.com/us-en/workstations/desktops/index.html
Z Workstation desktop PCs are high-performance and powerful PCs to help you from data processing to 3D rendering and editing.
www.hp.com
The two A6000 is enabled in part because actually are just dual width cards. similar board spacing issue with two Xeon sockets . but trying to stick to E-ATX sized form factor.
If AMD and Nvidia were pointing Apple at 350-400W cards (which the next gen seem to be heading for full steam) then it isn't surprising Apple is on path to dumping them.
The current design probably could support some water cooling if there was better routing from the Slot 1 and Slot 3 to the "empty void" where the 3.5" HDD drive bracket could be screwed in. If screwed in a custom radiator there with push-me , pull-you fans then could dump at least a card's worth there. ( high ingest temps from CPU cast off so limited. )
The other minor change to current baseline design would be some ability to provision U.2 to the optional add-in-drive bay. A PCI-e header along side or substitute for SATA header.
Another problem flying under the radar on the now older Mac Pro 2019 and its PCI-e v3 backbone data infrstructure is that PCI-e v4 (and up) don't travel as well when increase distances. So there is some tension to pull the GPU slots closer ( or have to augment with additional board complexity with re-drivers. )
For the consumer off the shelf space things are drifting toward just one big ( perhaps too big) GPU. Fewer doubles configurations ( AMD and Nvidia demphasising SLI/Crossfire in the mainstream) . And also fewer SSD add-in-cards. (mainstream boards having 2-4 M.2 slots. Workstations picking up U.2 provisioned bays. )
A PCI-e v4 x8 SSD add in card would cover the same bandwidth space as a x16 PCI-e v3 card in a future system. The baseline design that Apple has here will work when scale it up with better core backhaul. The full size MPX modules do some slot covering. But the MP 2019 board also has slots 6 and 7 as an offset in most circumstances.
The baseline standards for the PCI-e add-in-card standards and approach just really were not meant for 400w entities. It is a track that will run into more and more problems over time if there is dogmatic fixation with "do it with 80's and 90's tech". Can knock Apple's MP 2019 baseline design but Dell , HP , Lenovo , etc probably aren't going to 3 width spacing over time either over next 2-3 years .