All of this of course only makes sense for Win32 (cross) builds. On Unix we can only compile with vkd3d-shader and execute with vkd3d or Vulkan (and we already do both).
Yes, although a future where vkd3d supports additional Direct3D APIs doesn't seem that hard to imagine.
As I said, I feel rather maximalist, so in principle I'd implement all the lines above (though I acknowledge that some lines make more sense than others). Possibly with some options to disable some of them at runtime, for testing speed reasons. Also I'd rig things so that the non-cross builds is able to run all the combinations in a single executable, for convenience reasons.
Right, ultimately we'll probably want some more control at runtime over what specific configurations get run.