For a batch product I’d really consider making a jig. As these are rather tall objects you’re engraving, a throw away jig is not practical unless you have a lot of 12x20x1.5 inch boxes laying around. You could make one that fit in the four depressions that hold the crumb tray, or use some other registration point. I would expect placement under 1/10" with a removable jig.
There is another option. In your file make a tiny cross, or dot, or short line, and score it at power setting 2, speed 500. This will mark your masking and not go through it. You can use this to determine where the rest of your file will print. Once it is scoring where it should, ignore it and go ahead with your engraving.