This is the exact problem with the trashcan, it's a computer made for GPU computation (one of the trashcans GPUs isn't even hooked up to the display it's purely for computation) yet you are stuck with proprietary versions of GPUs that run the wrong sort of code.
Almost the entire GPU computing community works on CUDA, the trashcan cards don't run CUDA and because they're proprietary they can't be upgraded.
The right solutions are either this design or one where there is a heatsink+liquid cooling bracket system where you can attach a GPU after taking the stock cooler off to. Which is also very common thing to do for people in GPU computing. The latter invalidates your warranty so this design actually makes sense.
This design (even though it doesn't work in reality) is about creating something that is functionally like the earlier Mac Pros. That means commodity off-the-shelf hardware can be used, not just specialized or outlandish components that are going to be very expensive, if anybody bothered to produce them at all. The current Mac Pro still ships with the outdated GPUs it originally was introduced with, with no upgrade path foreseeable.
Here is an example of GPU improvements vs. CPU (although this is an older article) http://www.anandtech.com/show/7603/mac-pro-review-late-2013/...