Do stencil buffer can only be filled in by some hard-coded rules during geometry drawing (like depth buffer), or is it possible to fill it in completely programmatically with the help of full-screen fragment shader, which can for example draw black-and-white shape based on some 2D SDF?
Also is it possible to use stencil buffer separate of depth buffer in this case and don't use depth buffer at all?
You can output [[stencil]] decorated value from the fragment function, which is gonna be the stencil reference value according to Metal Shading Language specification table 5.7, and then set up MTLDepthStencilState in a way that stencil always succeeds. And set up the operation to be MTLStencilOperationReplace, which means
Replace the stencil value with the stencil reference value, [...]
which should make the stencil being effectively output by fragment function.