I believe that area is used to index the parts cut from the other sheet so that you can flip them over, drop them in the cut-out in the fixture area of the second sheet and then the router will cut the bearing counterbores on the backside of these few parts in the correct position.
So you'd cut all the parts out of the first sheet, put the second sheet on the CNC bed, make the cut-outs in the fixture area. Pause the CNC, drop the parts from the first sheet into the cut-outs (flipped), and then start the CNC again and cut the c'bores along with everything else on the second sheet.
That's my guess, anyway. Dan, or any of you other CNC jocks, please correct me if I'm wrong.