Standard-sized PCIe as a physical card architecture (as opposed to an internal bus architecture) is basically dead and buried already. I'll grant you limited choice in video cards, but otherwise, personally, I think you're putting too much emphasis on legacy hardware whose importance is waning. You'd have to come up with a new standard for motherboards, graphics cards, interconnects, and PSUs. There is no reason aside from inertia (and patents?) why DIY PC parts could not be oriented around a unified thermal core design. Hopefully it will get some PC manufacturers thinking about alternatives to the absurdly outdated ATX form factor. Overall this is a very clever and efficient design. So if someone is thinking about saving ~$1000 by buying the cheapest Mac Pro and adding the Xeon 12-core themselves, it might not be such a good idea. No matter how good Apple's engineering is, there's no way they managed to fit a 12-core Xeon and two power-hungry Tahiti GPUs within a 450W envelope. This also implies that upgraded Mac Pros must have a different, larger PSU. Take 300W for both GPUs, and another ~125W for the Xeon CPU, and you're pretty close to the limit. This one may be clocked lower, as is the case with the FirePro W7000 based on the same silicon, so let's say 150 watts maximum. The FirePro D300 is basically a professional version of the well-known Radeon HD 7870 gaming card, and that card has a TDP of 175 watts. Granted, most enthusiast PSUs are way over-specced (a hangover from the days when even major manufacturers blatantly lied about their wattage ratings), but that still sounds much smaller than I'd expect for a dual-GPU system.
Perhaps the most surprising thing to me when reading the iFixit article was that their Mac Pro's PSU was only 450 watts.
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