And it may very well be, I don't know for sure. But I think it could also be explained just by noting that if you're way out of the ordinary, you're probably going to have a lot of awkward interactions.
I lived in China for two years. Many times, locals made wrong assumptions about me. I guess I could have been offended about it, but it seems to be a fundamental part of our mental event loops to aggressively pattern match and categorize as quickly as possible, so I couldn't really get mad at people for doing it. I was/am way out of pattern, so I think some awkwardness is to be expected. (Now, I fully concede that what the author describes -- people initially not believing her explanations -- is one step worse. That really sucks.)
Have you ever approached a stranger and asked them something without somehow verifying beforehand that they would actually be able to hear you? Wouldn't it have felt a bit awkward if they'd been deaf? Would the incident really mean much?
I can imagine a hundred articles like this, e.g., "Actual words people say to a 162cm professional basketball player", and the main thing we could take from them is that people are on autopilot and you're in for trouble if there's something significantly different about you from what people were expecting.
"So you’re like genius? But you seem so down to earth!" "After you complete your degree, are you going into modeling?" "You don’t look like you go to MIT." "You look good!" and "But you’re wearing a dress!?"
The most specific comment refers to her clothing. It's not really a large enough sample to be sure, but it sounds more like people are responding to the care she puts into her appearance. Google image search tells me that this is indeed unusual for an MIT student.