I have found through my testing that the reference camera's layer mask is completely ignored. Unfortunately, this limits what map makers can do. I have run into this limit in a map I'm trying to make, which uses cameras rendering to render textures to implement effects; I'd like to be able to have different pens that do different things, by having an object in a layer that is invisible to all but my render-to-texture camera, but that seems to currently be impossible.
I realize that giving full control over the layer mask could cause problems, but there's ten unused layers (22-31) and I can see no reason why the reference camera shouldn't at least be able to disable those for player vision.