I think upgrades will only come from Apple.
For this specific model, Mac Pro 2013 , I don't think you'll even get them Apple.
Strongly suspect they haven't thought very deeply about how to do longitudinal upgrades, so there is no support for in this design.
Seems as though they may have "just enough" to get these cards out the door so that only two identical pairs work together well. That's it.
Longer term (and when "Crossfire" like feature is solely over PCI-e ) they may come up with a standard socket they can use over multiple generations, but that wouldn't show up until later Mac Pro designs.
If third party mfr's could barely be bothered to write Mac EFI for their existing PCIe reference cards, I just don't see them taking the even greater effort of making custom boards that are nMP compatible.
This. Not only the vendors though but issue even for Apple to engage in a upgrade service is whether there are enough folks who will actually pay for it. Lots of folks clamouring for 3rd party cards are primarily driven on cheaper than on paying for performance. They are anchored on "just as cheap as mainstream PC card" pricing and aren't going to move.
it is a combination of lack of demand and lack of supply. They are coupled because in part nobody wants to pay for the work for has to be done. It is just " give me at same cost as other cards that don't need the extra work/support/services or I'll go Win PC / Hackintosh / etc. "
As long as that is the dominate mindset there aren't going to be Apple or 3rd party cards.
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I should add I've heard rumblings of Apple thinking about possibly, maybe, Thunderbolt GPUs. I could see third parties doing that. Dunno how popular that would be though.
Again if run into the buzzsaw of folks wanting Thunderbolt aware drivers but then not willing to pay for the work ..... going to be waiting a long time.
Over time I suspect someone will come up with a list of kludges and hacks to make this appear to work. That will be the "cheap" way and no supported market will surface because what is left over is too small.
Might grow the Mac GPU market a lot if Macbook Pro, iMac, and Mac Mini owners could partake.
Demand from that foundation will be dependent upon "older" thunderbolt enabled models. Those models have another couple years before that large fraction of that base considers them "older and problematical"