The longer answer is this:
When the body is a blank, they drill registration holes in each side. The registration holes mount on pegs that stand proud of the CNC table surface. This keeps the body lined up in the correct place on the CNC table so everything gets cut in the right place. The back is routed first. Then they flip it over. The registration holes on the front of the guitar (which hold the body in place for the back routing) are destroyed when the CNC cuts the frontside, so they cannot flip it back over for more cutting on the back and be assured of everything lining up.