You have to do the alignment marks at the same distance from the camera as the item you are engraving. The camera alignment is only accurate for the height that the markers were done at. The system is designed to work with a laser that has a Z bed that raises and lowers, so the top of the material is always the same distance from the camera.
It is possible to run the alignment marks on a piece of material that is lifted to a specific height, then save that calibration by right-clicking in the Camera Control window and saving it with the height in the name. If you use 3mm, 6mm, 9mm, 12mm material, you can just save one alignment for each height and then Import the correct one when changing material thickness.