I have flown repeatedly in the last two months, and I have not gone through a body scanner yet. Though they have them airports, they often aren't using them or use them for only a small percentage of people.
I was binding, packing, and even passing as a male and flying on F ID without any problem. I *did* have a carry letter from my therapist, just in case someone asked (no one did).
I also knew that if I did have to go through a body scanner, I could either opt out and ask for pat down OR let them scan me, knowing that they'd prob ask me for a pat down anyway (due to the packer). It never happened, though.
In the months prior, though, I was dressing more andro to pass as female, didn't have facial hair (like I did more recently), and I would keep my packer in my carryon. I would go through security not packing and then just put it back in the first bathroom after security.
It's really about how you feel most comfortable. They are far more likely to flag you for being twitchy and weird than anything else.