Thanks everyone so far for sharing all your experiences.
Jill's first link seems to answer the question from TSA's POV...
QuotePat-Down: A pat-down may be performed if there is an alarm of the metal detector, if an anomaly is detected using advanced imaging technology, if an officer determines that the traveller is wearing non-form fitting clothing, or on a random basis. If a pat-down is chosen or otherwise necessary, private screening may be requested. Pat-downs are conducted by an officer of the same gender as presented by the individual at the checkpoint.
I guess my friend's concern was partly from that she was presenting fairly androgynously. After being patted down somewhat "closely" by the female officer she got a very black look. Not sure whether the female officer didn't like the fact she was MTF or had re-evaluated her as cis-male and was a bit put out.
