I think this is more a matter of preference. The Z-axis is controlled directly by 2 stepper motors on lead screws, so it is very precise. If you measure the material accurately and set the Z-home precisely, then I don’t think there’s actually much of a reason to cut deeper. Building a Z-probe will help a ton with setting the Z-home precisely (Instructions - How To Make And Set Up A Z-Probe On The M4). And if a cut doesn’t go all the way through, you can try running a sander over the underside of the cuts until it gives way.
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