Can you just generate code to follow the line and edit the code by hand for your clearance moves?
Not only for the clearance moves, all value must be changed. (moved and reverted)
CamBam generate only toolpaths from Stock Surface to 0.
ex, the pink line is used to define the mop

If I set Stock Surface to 15 the path is Ok for the last pass but not for roughing.

to solve that, I move the polyline so the max diameter is at 0, then I add a toolpath transformation to move the toolpath at the right position.(in Y)

And now a scale -1 (invert) to revert the toolpath to the right side.

That looks OK on the display, but unfortunately all the matrix transformations are ignored when the Gcode is generated.

++
David