Make your Z zero the bottom of the plate, NOT the top of the plate. Many people don't realize this, but this way the thickness will be exactly what you want after you face the material/part.

For example, the Z Zero on my Robodrill is the vise bed, and it will never change from that. I will never put a probe in my Robodrill again, there is no need, draw everything in CAD so it comes out EXACTLY as planned.