I’m not understanding how you are heightmapping. It sounds like your mill is not level with your workpiece. You can level the machine bed to the the gantry motion or you can try and change the machine motion (not often easy).
The 3018 is a bed slinger like many 3d printers, but the mounts on it are not centralized, they are connected on each end. if the table it sits on is not flat, it can rack and the motion of the bed will not be in a flat plane. I’d start with the table the machine sits on. Ensure the table is flat. For example, the shelf thing my large 3d printer sits on is not flat. shim a foot or two to get close. Check that the machine feet are all the same, then loosen the frame bolts and let the machine relax to the flat table top, then tighten it back down, then do the wood spoil board planing.
Typically a piece of sacrificial wood is used as a base “spoil board.” A piece of mdf is easy to cut and if not super humid, will hold it shape. You then surface that wood to be level with the machine, attach your copper-clad board to that piece, and run your operation on the workpiece. Probing then only needs to be done once at any location on the board to set the z height. With everything cut flat, the assumption that is all level should then be correct.
Out of curiosity, how thick is your copper and how thick is your soldermask? Have you tried cutting a thin aluminum plate to use instead? I’ve had laser-cut stainless steel masks made that lay over the top of the board as a solder stencil (perhaps that method could work?), but most optical masking like the one you describe that I have used are done with photoresist and then chemically etched to produce the circuit openings and typically at a much smaller scale than a mill bit would allow.