I can't tell if TSA acted inappropriately here from the article. But if the trans distinction is an issue that they may run into, they need procedures to deal with it respectfully.

But I believe accommodations should be made if they are reasonable.
We're over here talking about calibration like we know what the hell we're talking about.

If it's as easy as you say it is, then sure, do it. Fix the machines to deal with these cases.

But if it is not so simple, why invest so much effort (and money) in something that be resolved with existing technology?

In this situation maybe they could be more discreet. Or hell, don't tell her anything. Just tell her go through the machine again (no explanation necessary).
Everyone here had no idea the screen differently for men and women. Why tell her?