A suggestion - Use a leadin/leadout like the plasma folks do. If you are trying to cut a disk, start and finish with a move that takes you outside the toolpath for the disk. If you are cutting holes, start on the inside and have starting and ending moves that take you to the inside of the finish hole. You might still come up with a slight mark where the cuts overlap, but if you play with how much under/over cut you do at that point you can minimize it.