I think Michelle has a sensible suggestion - I wasn't aware the US TSA published a Medical Notification Card format.
Other countries probably have something similar, or you can re-use this one until they do. A card like that allows you to inform security if you decide to do so, without making a public announcement.
I have traveled quite a bit including international, and have occasionally run into frustrations that have nothing to do with gender. And this reminds me - on a flight from Los Angeles to Sydney, a male co-worker I was traveling with was stopped at the security line. TSA informed him loudly enough I could hear their exact words: "sir you have an anomaly in your pants". He broke out laughing, but then quieted down when he realized it ain't a good place to start joking around. Nothing major happened, they did the pat-down as he stood there silently with a "yeah so I am well endowed down there" smirk. There was nothing in his pants, other than what he was born with. This was 5 years ago before machines were upgraded and US TSA procedures improved. If he had made a scene or refused to be patted down, he probably would have been stuck there with his anomaly.
Other forms of prejudice have caused people to make calculated sacrifices with great social impact - for example getting arrested for refusing to sit in the back of the bus, or interracial marriage (when I was born, my existence was a felony in several US states). But I don't think missing a flight will cause any meaningful improvement in the way transgender people are treated. I am not trying to downplay the frustration of things that can and do happen, but I follow the security rules and do my best to keep the line moving.