So I needed to understand how Processing draws complex shapes. The reference describes an important aspect of the beginShape/beginContour function "The vertices that define a negative shape must "wind" in the opposite direction from the exterior shape. First draw vertices for the exterior shape in clockwise order, then for internal shapes, draw vertices counterclockwise."
So I tried 'cutting' a circle out of a flat rectangle (red stroke and white fill kinda shows what is going on).
This gave me the idea of making my life a bit easier and flattening the top of the base cylinder in the CPAP model so I could use a modified version of my testing code from the above example.