If I assumed any woman wearing pants and a tshirt wants to be called a man, I'd offend them more often than not. Guessing somebody is transgender because they aren't conforming to gendered fashion conventions is an extremely bad idea.
The parent wasn't just talking about the top-level of their clothes, though, but about overall presentation. There's generally a lot more cultural signifiers embedded that you can cue off of than just "pants or skirt?" after all. Haircuts (highly gendered even at similar lengths), subtleties of makeup and jewelry, the cut of the aforementioned t-shirt and pants, body language, etc. (And there's still room to get it wrong, of course. But fortunately people who're living in the gray areas are generally aware they're doing so.)
Explaining all the details of how to distinguish e.g. a butch lesbian from a trans man to someone from a different cultural tradition is, of course, an incredible pain.
I've known plenty of women with male or gender neutral clothing, "boy cut" hair and no interest in jewelry. They weren't men. Assuming that a woman is transgender because she isn't "girly" is idiotic.
The number of people, particularly women, who don't adhere to gendered fashion greatly exceeds the number of transgender people.
