The stock z-zero in CC settings seems misplaced because whether a carve is relative to the top or bottom of the stock seems like the property of a toolpath, not the design or the model. More importantly, making the z-zero setting a property of the stock is inconvenient when a project involves both top and bottom z-zero toolpaths. Since wood thickness varies, I find it safer to use the top of stock for things like VCarves. However, my projects typically end with a toolpath to cut out the object. I like to call this last toolpath “perimeter” because it encloses the final product, perhaps with tabs. I tend to preserve spoil board a bit with a bottom z-zero setting for perimeter toolpaths. (Trust me, I already have enough divots in the spoil board of my own making. 
) Of course, CCP permits exporting G-code and changing the settings, but it means leaving the toolpath window to the design window, often deselecting some shape, changing the setting, then returning to export the G-code. This workflow is often followed by undoing, i.e., reversing the workflow I just described. In addition I need to remember which setting is in the c2d file and keep flipping the settings if I need to make changes to the G-code. At best this is a needless nuisance, and at worst I make errors through forgetfulness.
I’m aware that all of us CC users have been trained to setup our stock (top/bottom z-zero) in this way. So I propsose a compromise. Leave the top/bottom setting unchanged and treat it as the default. Add the same top/bottom selection pull-down to each toolpath creation/edit window, and use the stock’s setting as an initial default; but allow the user to override by making the alternative selection. In this way the top/bottom z-zero setting can be stored in the toolpath configuration where it naturally belongs.