If you have surfaced your spoil board you can reference the spoil board instead of the top the wood and get a cut that just barely cuts through the wood. That might help. I’m linking a post of mine that has a video on how to do it.
To sum it up you either set Z0 to the spoil board in your CAD/CAM and machine or keep Z0 at the material surface in CAD/CAM and set the Z with the paper method on the spoil board but instead of hitting the zero Z button you click on the Z number and enter -material thickness. So if your wood is 3/4" and you set the height of the spoil board to -0.75" then zero is at the top of the wood. This cuts out the error from uneven wood and because you surfaced the spoil board you can get accurate through cuts.
It works well enough that I can keep the laser job on my spoil board for a long time.