Maybe there should be a subject change. Have a look at the two fixtures whose photos I've attached.
I make printed circuits which are about 2 inch by 3 inch. I found that I couldn't get reliable trace widths unless the board was absolutely level to the machine. So I started with an MDF fixture bolted to the milling table and drilled and tapped in four places so I could use nylon screws to hold the pcb down. Every time I do a new setup, I mill the surface of the fixture with a fly-cutter to level it. This works 100% of the time. I've had no bad experience with PCB's not being of constant thickness.
I had such good luck with the MDF board that I made a better one for HDPE. I also made a jig to drill the holes in the pcb so they would be sure to align with the ones in the fixture.
Frankly, I don't see how you could ever get reliable cuts without leveling the surface the pcb is secured to while etching.