When creating a setup and defining the stock in the Stock tab by default the Mode selection for Fixed Size Box and Relative Size Box include all solid bodies in the model ignoring the current Visibility settings in the model. The visibility settings in the model workspace don't appear to be used in the CAM workspace. For sure not when creating a setup and probably elsewhere. The only option which allows you to override this is the "Form Solid" option which allows you to select only the solids you want to be included. I would consider this a work around and not the correct behavior. Also the stock selection is ignored when creating a 3D toolpath, 3D Contour specifically. I'll create a separate suggestion for this.
