it is common practice on a mill / router to have 2 sets of coordinates
Machine and Work
Software controllers like Mach3 and EMC will have these functions built in,
and I would lean towards a similar setup / routine which seems to work well
Once the machine is homed, you can define or set the maximum travel allowed ( machine coordinates.)
then it’s switched over to work coordinates. where you can zero the cords. where you need to on your part,
you mill and cut in Work coordinates
while your machine coordinates keeps track of your maximum table size, in the background