Instead of doing the extrude in rhino, I made the extrude of the offset in Grasshopper and put it on a slider to give me control over it. Two options are shown below. I then tried to do a cap of the outside shape and a cap of the inside shape (the offset) and then boolean difference those in Grasshopper. It worked correctly on only the third box. Not quite sure why… I ended up baking the extrudes (no caps) and then planar surfacing in Rhino to cap the open edges.