I recently flew from Logan airport in Boston and wanted to share the experience with anyone concerned about the process.

After putting my shoes, electronics, and bag in totes for x-ray I was directed to the body scanner. The  operator motioned me into a giant phone booth and had me put my feet on yellow footprints on the floor and raise both hands over my head. As he prepared to exit I said "I'm transgender." and without slowing down he said "No problem, miss."  The door closed, the scanning bar passed in front of me and he waved me out the other side with "Have a nice trip, ma'am." 

The way it was set up, there was sufficient privacy to discreetly inform only the machine operator of my status. I  feel that the whole process was a non-event in comparison to some of the accounts I've seen. I'm only speaking for myself, the operator I encountered, and this one particular trip from Boston. YMMV.

  I fly a lot and to facilitate the check applied for a TSA PRE , applied Friday and had the number on Monday morning.  It cuts the waiting time way down and you dont have to do the things the regular line does. Only problem I have ever had was when I was wearing a lot of jewelry then they just checked it. There was never a question asked about my gender and I never said a thing about it. Great experience , TSA PRE is the way to go . 

I guess I am lucky with that experience. My wife works for an airline and we travel often. Just came back from Cali last week. But when I go through the phone booth I tell them I have a pace maker, then they see abnormalities on the other side and I tell them the leads are still implanted in the other side. It will be a problem soon as I will no longer be able to wear sweatshirts in 90 degree heat. We go thru the tsa pre line so it is not as stringent. I do still have my Nexus card which gives me known traveler status. I use that to enter Canada, but it also serves as a photo ID.