I think it would make more sense to do something similar to MatterControl and have CAD functionality inside the slicer. This would make it easier to do specific things like aligning "change at layer" or modifier meshes to locations of the imported part. This also removes the expectation that the CAD functionality would grow to the state of FreeCAD or Fusion360 where there are features adjacent to 3D modelling for 3D printing, such as 2D drawings and... uh... well I'm sure there's many features I don't even know about that wouldn't be applicable for additive/subtractive manufacturing. 

Additionally, merging the projects means that model features / files that are only designed to aid in CAM will not have to be exported and imported from program to program.