When I make a toolpath with a ball end cutter, the toolpath is drawn at a height above the model which is the radius of the cutter. The toolpath with a flat end cutter is what I would expect - it is on the model.

If the top clipping plane is below the radius of the cutter, nothing is cut. What I expect is that the toolpath would be drawn as the bottom tip of the cutter and this would be what the clipping plane would be associated with.