In theory if DirectX games start passing shaders to the driver in SPIR-V, the same format Vulkan uses, then yes it should make Protons job easier. Translating the current DXIL format to SPIR-V is apparently non-trivial to say the least:
It's unlikely to diverge from the same general flavor as vulkan. The worst parts of the DXIL to SPIR-V conversion I remember from that chain of blog posts is rebuilding structured control flow and how it interacts with atomics and wave convergence.
That's a problem that goes away irrespective of any DX extensions to SPIR-V for supporting the binding model DX uses.
