I would have the offset set to center of the axis, not stock surface. You have a tool zero, and then you program the offset to the center of the axis from there. Designing parts is no harder. You just set your stock surface at the starting radius of your stock in CAM.

I know, in ordinary 3 axis milling we usually set stock surface to zero, but we don't have to. We can use whatever is convenient for the machine setup or the part geometry.

Anyway, I am muddying the waters and probably not helping the OP by going off on this tangent.