If the Add or Subtract brush blending modes are set, this enables the user to paint only on active channels quite easily. Note: At the time of writing, Blender 2.80 does not support rendering or painting with vertex alpha, but the alpha values are stored in the vertex color data correctly...
To subtract mesh from a face set, you do the same but instead of hovering your cursor over a face set you hover it over geometry that isn't part of a face set or outside your object altogether. Now when we have face sets and some basic control over them, we can start to hide geo...