Hey Jim,
it is not the controller that “wants” to do that. The controller just executes your g-code program, and if your g-code program contains such a home command at the end, the controller can’t do something about it. See here.
If you already finished your enclosure, I think it will be no help to you if I say, when designing an enclosure, be sure to allow for dust boot overhang
A few links to dimensions useful for dimensioning table/enclosure/wasteboard
Welcome to the forum!