[AtlUmpSteve]

Seems to me you answered at least part of your own question.

By telling her she wasn't in the batter's box, the umpire was stating she was not, in his opinion, in the box, no matter what doubt she may have had. To him, that was completely obvious.

The umpire does not need to measure or remark the box at the batter's request; the batter needs to comply, or be subject to "out of the batter's box" rules. That means strikes called every 10 seconds without a pitch being thrown until she does get in the batter's box as directed (ASA 7.3-C).

You may consider it her right to have a different idea of where the batter's box line is; the fact is, what you are asking is if she has the right to both show up and defy the umpire's judgment and direction. At least, that is how I look at batters that want to tell me I have to draw them a line; and that is how they were treated in return.

I have had several batters take strike one; in 30+ years of umpiring, I've only ever had two batters stand there and take strike two, and no one has been defiant enough to not find the batter's box before strike three (although one was bailed out by her coach asking for time to tell her I wasn't playing).