I think that from a software perspective, the problem isn't patented hardware. It's secret hardware. A lot of what's in current GPUs is undocumented and treated as a commercial secret or disclosed only under a non-disclosure agreement, meaning you can't write open software to use it other than if you can reverse-engineer its function.
Why do GPU manufacturers keep their chip internals secret? One explanation is that since they can't patent the techniques they are using (because of prior art), they fall back on secrecy. Another is that they *know* that they are violating someone else's IP and don't want that someone else to find out! And of course there are closed-ecosystem cartel / monopoly / NSA-backdoor / conspiracy theories too.