Reading it again, it looks like hyperbole and he's using the 'proprietary software' phrase to mean opaque to understanding by everyone other than the core developers, but it could also include the possibility of actual proprietary components which would (intentionally or unintentionally) tie the algorithm to some specific private hardware or software intellectual property or trade secret.

It could mean either or both. Proprietary could mean the GPU supplier's custom acceleration facilities and drivers. It could also be a poor choice of words given his background in developing custom software which typically is referred as proprietary. In either case, there is something nonstandard about both, and this is what I think he's objecting to.