Flying while transgender — a term that increasingly includes not just those who are male or female but also those who identify as both or neither, like me — is undeniably improving. Last month, United Airlines expanded its gender options: Passengers can select male, female, undisclosed or unspecified, and can choose the honorific “Mx.” “Fly how you identify,” the airline touted in its feel-good tweet — and American Airlines, Southwest Airlines, Delta Air Lines and Alaska Airlines quickly promised they’d make similar changes.

But it’s not actually possible to “fly as you identify” as long as the Transportation Security Administration screening process relies on the idea of binary gender. As the T.S.A.’s own guidelines state, “When you enter the imaging portal, the T.S.A. agent presses a button designating a gender (male/female) based on how you present yourself” — that is, how the agent perceives you as presenting yourself. This selection triggers expectations that guide the screening process. If, for example, an agent presses the pink “female” button for someone wearing boxers, an alarm will be triggered on the scanner, because loose fabric around the crotch of a female body is considered unexpectedly gender nonconforming. A compression shirt on the chest of someone for whom an agent presses the blue “male” button can do the same.

Once gender has been chosen, the machine proceeds on expectations about anatomy. A transgender passenger who passes — who is correctly read by the T.S.A. agent as the gender the person identifies as — but who has different genitalia will trigger an alarm. Intersex people may have ambiguous genitalia that trigger alarms and require invasive pat-downs every time.

In 2015, when Shadi Petosky’s horrific experience gave rise to the hashtag #travelingwhiletrans, the T.S.A. still classified the genitalia of transgender people as “anomalies.” After the outcry, they now use the new language of “alarm.” Current T.S.A. guidelines state that “agents are trained to clear the alarm, not the individual.” But when identity and body cause the alarm, what’s the distinction?