Octane Render for example is a pure CUDA 3D rendering software, meaning they'll be relying on Nvidia to be the dominant workstation GPU market holder, but if someday AMD somehow manages to beat Nvidia, Octane is pretty much in trouble, and switching their software 3D kernel isn't exactly an easy thing as they'll have to do a converter for old files and bla bla bla.
A. not sure why their file format would be hard coupled to GPU architecture. It is just data. And frankly the GPU architecture is likely to change substantially over the next 5 years even if they stick with Nvidia. There is no good reason to tightly couple those.
B. the model that they are relying on is not so much "X beating Y" but of dictating to the customer which hardware they buy. The dependency they have is that dictation is an option. If market went to Intel and AMD having 60% of the graphics market and Nvidia having 40% they could still tell their users to go buy Nvidia cards and systems that take those cards.
In the OS X space, that was an illusion that they were in charge of configuring systems. They can retreat into Windows and Linux and survive but if being multiplatform was a goal tying themselves to a single GPU is an inherent conflict.
Here is where most PCs are going....

http://anandtech.com/show/7677/amd-kaveri-review-a8-7600-a10-7850k/2
Are "Workstations" going to rebuff the APU trend for a very long time. Perhaps. But that is awful lot of folks who their competitors can sell to that basically have locked themselves out of. People tend to stick with what they learn on.
Now that we're talking about this, I wonder could this be the very reason why most 3D rendering software is still CPU based?
In part. If restrict yourself to x86 PCs there are alot of them. There is also limitations in just how "general purpose" GPGPUs are. Up until recently that was an extremely generous characterization ( really were fully general purpose.). Increasingly adding more reasonably good scalar abilities and access to main RAM memory store.