In fact, using the men's room dressed that way could have been dangerous for him. However, since women's bathrooms have stalls, and there is no need to expose oneself, I say let him use the bathroom he is most comfortable with. The writer was upset because a man, dressed as a woman, had used the ladies restroom. You said the person could have been a woman who simply looked masculine or could have been a crossdresser, in which case he should use the restroom he is most comfortable in. This man also may have been a transsexual - meaning he was born male, but is living as a female.
Transsexuals have a difficult time coming out in our society.
They often lose their jobs, their spouses, their children, friends and families. Their suicide rate is alarmingly high. I am not a sexual deviant or a child molester. Transsexuals are average people trying to achieve some degree of normalcy and happiness. Your readers may sit next to us on the bus or work in the same office and never know.