Well I don't know all the facts about your workflow. I suspect you've tweaked something else along the way, to make it work with the wrong scale setting. But I don't know enough about either your workflow, or what the workflow should be (since I don't have any kind of cutter, or use gcode at all).
It doesn't make sense to change the programming to fit your workflow. It makes more sense to correct the workflow. Unfortunately I'm not the best person to sort out what you might have tweaked to make it work. And I certainly can't tell you how to edit the program files (PY file). (because I don't know how)
All I know is that by using the correct scale, there is some way to make your drawing cut at the right size. I just can't tell you exactly what needs to happen. But hopefully someone else will be along, who can help.