It can order cuts by color or layer. It's kinda nice for me, when doing multiple sets of hours, I can color each one a different color, set it up to hold jobs, click one each color with crosscut turned on, then hit send. This way I get 12 sets of vinyl, each cut apart.
Ideally instead of coloring a shape white, you would combine the two shapes into one. In corel it's called combine, not sure what illustrator calls it. In my world, I curse at the designer who just draws white boxes instead of properly creating graphics with voids. Not sure how many others around here expect their art to come to them, but I expect some others have the same opinion. It's a lazy way to build things in my opinion.