Even with no batter's box chalked out, all of the rules pertaining to the batter's box still apply. But, with no lines to go by, the umpire should give every benefit of the doubt to the batter. This isn't a call that an umpire should be itching to make. It should only be called for gross, blatant or obvious violations.
The softball batter's box extends 48" forward from the center of the plate, or 39.5" from the front edge of the plate. Batters have a lot of room to move around and work with! If you try to lay that out with a bat, well, good luck finding a 39.5" long bat. You inevitably will be chopping at least 6 inches off the front of the box- enough that your line scratched in the dirt could make a perfectly legal batter "illegal".
Laying out lines on the field is the responsibility of the grounds crew, not the umpire. If you don't have the tools to lay it out the right way, you can be creating more problems than you're solving. Scratching lines in the dirt is not something that is recommended in any umpire guidelines or training and is a poor practice.
If there is a box laid out, but it is not the right dimensions, the umpire should wipe out the misdrawn lines and either have them corrected or, if that's not practical, use his best judgment as to where the actual lines should be.
Even without lines, it is pretty easy to see when a batter sets up too close to the side of the plate. The box is 6 inches away from the side of the plate, and if you see a hitter set up with her toes almost touching the plate, she is obviously out of the box. That is about the only time I will ever ask a hitter to move back off the plate- when it is blatantly obvious.
The box is 7 feet long, front to back. A slapper has a lot of real estate to cover before she is out of the box.
Calling a batter out for being out of the box should be a very rare call. The plate umpire has about a half-dozen other priorities and being out of the box is low on the list. The ball or strike call in relation to the strike zone is the top priority. He is also watching for illegal pitches, the batter contacting the pitch, the pitch possibly contacting the batter, a "swing/no swing" call on a checked swing, possible interference by the batter or catcher obstruction.
Even with the lines correctly drawn this is a low priority call that needs to be blatantly obvious to call it!