the way to try this, is to turn off the power to the machine, and by hand, move the X beam (gantry) all the way to the back. That is obviously as far back as it will go.
If the hole you’re trying to make is behind that (or any other part of the cut) bad things happen.
Specifically, the machine THINKS it’s moving further back, say 1", but physically it is not (the stepper motors end up dropping some steps)… which is not nice. but worse, once it later moves forward that 1" again, it actually moves that 1" forward. So now there is a 1" difference between where you zeroed and where the machine actually is… and all cuts now are off by 1"
Now, the shapeoko might not be able to cut all the way to the very back as you might think if you look at the wasteboard… but it can cut forward a lot more than you think as well… so you can overhang on the front side…
(think of it this way… the router is to the front of that beam)