Just to confirm…Is it correct to say that during a STL import if I set the Z distance to the height of the model (base to max height) along with X-Y scale, then the model with be full size (x,y,z). When machining the second side, it seems there will need to be an offset from the baseline to keep the second toolpath from overlapping on the second side and to get the correct shape and this would depend on the model and stock size.
You would want to model the STL to full thickness/height, but then you would want to limit the depth of toolpaths so as to keep from cutting through prematurely.
You might want to consider using MeshCAM instead since it has specific support for two-sided cutting.