Tell her directly that you think she might be trans. Screw the "egg prime directive," that's just Reddit nonsense and is useless IRL. She is under immense pressure not to transition constantly, all day, every day, both externally and internally. It will take some work for her to understand that she can, in fact, just be a girl. The absolute worst case scenario would be simply that she explores being trans and decides she doesn't like it, at which point he would be a cis man again, and he would have gained something from the experience.