This is true. However, Apple just announced that the 2018 Mac Pro will be modular/upgradeable. So that definitely suggests non-proprietary PCI-E, which would be amazing!
The 2009-2012 Mac Pro had a modular processor tray. That was proprietary. Commodity parts and modular parts are two different dimensions. Apple leveraged a tray so that could do both dual and single socket CPU package system with same infrastructure.
Have about the same issue now. Only Apple has extremely likely committed to single CPU package; so no CPU tray. That roadblock Apple hit was needs more commonality between one and two GPU systems. Apple could easily solve that with a customer GPU tray in basically the same way.
The other huge assumption you are making is that Apple is going to take a huge shift and not pump the display port output through Type C sockets like every other Mac that has been updated in last year or so. Thunderbolt output is highly likely (The Macbook is the only odd-ball non TB system and that's highly likely to change on the next upgrade). In that context, a pragmatically embedded GPU is also likely.
The shift to more generic standard physical PCI-e socket would only be the case if Apple had decided to get out of the GPU card design business. There is nothing in the statements they made today to support that in the slightest. Apple got 'stuck' putting custom cards into their own custom case. Honestly, there is something a little screwy with that story. Everything they described about loosening the integration to make it easier to design something that is upgradable more often would just make their custom work easier. That isn't punting the work completely off to others.
If Apple got "stuck" because there is chronic lack of resources to get a wide variety of custom GPU cards done in-house then perhaps they will punt. The trend line in every other Mac system though is for Apple to do their own GPU board work. But that may leave them overloaded to cover the Mac Pro.
This means NVIDIA still has incentive to develop drivers for Mac, because consumers can buy their cards and add them to the Mac Pro, just like with the old Mac Pro tower.
Only if Apple is getting out of the business of doing GPU cards. Apple was luke warm in this session to the external GPU issue and as long as Nvidia can't win a design bake off for an Apple system ..... things aren't necessarily going to be better for Nvidia.
Drivers for just the Mac Pro isn't really alot of incentive. From the numbers given in the session from Grubers article
"... Even among pro users, notebooks are by far the most popular Macs. In second place are iMacs. The Mac Pro is third. Apple declined to describe the Mac Pro’s share of all Mac sales any more specifically than “a single-digit percent”, but my gut feeling is that the single digit is a lot closer to 1 than it is to 9. ... "
I'd go farther than that in that Mac Pro percentage is probably closer to 1 than it is to 0. It is doubtful the Mac Pro is anywhere near 9 percent unless cobbling together Mac Pros over a 10 year span of sales. Apple has about 6-7% of classic PC market space. 1% of 7% is approximately zero. Even 9% of 7% is essentially zero. The Mac Pro all by itself can't drive a robust GPU card market. The ecosystem even back in the 2009-2012 era was a race-to-the-bottom market where one vendor would do a Mac card and there there was a huge raft of other copying the work cutting them off from return on investment. It is likely one reason why Apple when custom with the Mac Pro 2013 ( beside the TB issues. ).[/QUOTE]