The main issue with PCB milling is that the board will not be flat. Whatever clamping arrangement
you use typical FR4 board you obtain will be slightly curved and not quite flat in the bed.
This means you have to probe the surface to get its geometry first, then mill the traces.
We had such a setup at our Makespace, using one of the cheap chinese PCB mill CNC machines
and LinuxCNC. The only reasonably reliable approach was to use a fresh carbide engraving bit
on every board - even a small amount of wear means the bits snag the surface of the copper.
Any movement in the clamping system meant a bad job. The Z-axis backlash was never fully
elminated and the machine fell out of use.
Separately I've experimented using pointier bits (Z axis error less critical), which can help, but the
blunt bit and curved board issues are the big ones.
With CNC you drill to the smallest size with CNC, and hand enlarge any holes that need to be bigger,
rather than endless tool-changes and z-recalibrations.