That's what the red button is for. When you are done setting the Z height you can push the red button. That sets the origin for the height just like a probe would. I was experimenting with cutting in two passes with a z height adjustment in between. You've gotten better results than I did Garrett.
Other ideas are to lower the Z axis for thicker shading lines.
You could put some acrylic on supports, cut a shape, lower the bed, and melt part of the piece. Say, cut a flower then bend the petals.