I flew out of Hartsfield-Jackson Atlanta International last week, and did go through the full body scanner, but I had figured I would have to before hand, so I had put my packer in my checked luggage for the trip home. My originating airport in Dayton, Ohio doesn't use them so I wore it for that first flight.
In Atlanta, the body scanner wasn't mandatory, but it also wasn't obvious which line went to it. I was already in queue for it by the time I realized it was different from the normal metal detector lines, and I figured backing out would garner more suspicion and warrant a full pat-down, which could have been very awkward since they would first see me as male and then notice what I was missing face-to-face. My understanding prior to my trip after doing a bit of research on it was that the people viewing the monitors for the full-body scanners can't see the person except for the image on the scanner. So they wouldn't necessarily know for sure if the person in the image that they're looking at is presenting as male or female. They also don't see a name, gender, or any other info from the person's ID to accompany the image. They're looking for contraband, no reason for them to complicate things by looking for something that's 'supposed' to be there but isn't. That's why I thought not packing was probably better for escaping notice, but to each his own.
I had no problems, by the way. It was quicker than the metal detector lines, I was through in 5 minutes, versus about 20 for the metal detectors. They did pat down my chest briefly (was binding), and the low cargo pockets of my loose shorts after the scan, but they did the same to the guy who was behind me too. If they noticed the binding, they said nothing. My ID says male now too. I was pretty nervous, to be honest, but letting myself appear so could have been disastrous. I recommend doing whatever you're most comfortable with. I've heard TSA employees have had training regarding transgender rights, but there's varying accounts of their actual treatment of us.
