What are we supposed to do instead?
Only useful thing I can think of is treating these as unbound resources and returning 0 for reads / discarding stores, but that's going to be a huge amount of work given the mess that vkd3d-shader currently is. And it's technically not even our bug.
Native drivers fail compilation if root signature is broken. The fix in vkd3d-shader is pretty trivial, it just needs to check for error condition before returning.
Nothing extracted yet.
If we miss a binding in the root signature, DXBC backend will not fail compilation and we end up hitting driver with broken SPIR-V.