I'm not sure what might be the problem. What you describe is absolutely possible, so the question becomes what stops you from moving the vertices individually? Make sure to use the move tool to edit the vertices and deselect the mask before selecting individual points, otherwise you'll always move the entire mask, which with the stopwatch enabled will of course make the whole block bounce around in an unnatural manner. Unlike with painting, you will also have to have a duplicate of the structure underneath the layer you edit, so it fills the resulting "hole" from the masking. In your case you need to switch the mask from its default "Add" to "Subtract" mode.