A preprocessor step mostly solves this one. No one said that the shader source has to go into the GPU API 1:1.

Basically do what most engines do - have preprocessor constants and use different paths based on what attributes you need.

I also don't see how separated pipeline stages are against this - you already have this functionality in existing APIs where you can swap different stages individually. Some changes might need a fixup from the driver side, but nothing which can't be added in this proposed API's `gpuSetPipeline` implementation...