I use the "place registration marks" option from the objects dropdown menu, when I have the objects selected. It adds 4 into your design, and I simply delete the bottom 2. This also allows you to resize them as needed, and place them anywhere else you like, such as closer to the design to save some vinyl.
I don't use the checkbox in the cut dialog. As you said, it makes 4 of them and I don't use the bottom ones, although I've been debating toying with it to see how much better it works for actual registration!