Ignore the last response, the pasted link was incorrect and meant for another email reply. I included the correct link in this reply.
Have you gone through the alignment modes documentation and videos? Modes 2,3 or 4 will align the bottom of the cutout, regardless of what the bottom is. Use one of these. All 3 will align tot he bottom of the cutout but the differences will basically be the left-right alignment as described in the tutorials in this link.