I'd suggest that problem is self-correcting. If for some inscrutable reason this otherwise normal kid decides to get his ID in drag, then every time he needs ID it's going to cause him problems. If this kid is normally in drag and is forced to forced to have his ID picture in normal male attire sans makeup, then every time he needs ID it's going to cause him problems. Only if he is conspiring to commit a crime and/or make an escape in normal male attire sans makeup is this going to be a problem for government, and one could make an argument that straight boys could even more easily commit crimes and/or make escapes in drag with normal ID photos. Certainly an otherwise normal young man would be a less likely suspect in an apparently female-committed crime than is a young man in drag in an apparently male-committed crime. Hell, they're probably looking for something with which to charge him anyway.
Just because the knee jerks does not mean the knee is necessarily correct.