takitus has it exactly right.
Note that we don’t focus the lid camera differently with the thickness number: we use the height to dewarp the image so that the preview is correctly aligned with the cutlines. We basically add that number to the bed height to determine how close the surface of the material is to the camera.
When people have alignment problems, it’s often some tiny bump of something raising up the material just a bit, so it’s closer to the camera than the thickness measurement would indicate.
Working around this is one of the biggest improvements we’ll make to camera alignment. We’ll do it by making a quick surface height measurement with the red dot laser before we dewarp.