When I was in elementary school there were two “Tony”’s in my class. One was a boy, one was a girl. It is possible that the girl might have spelled it “Toni” (I do not think that it ever occurred to me to ask).
I have known three “Jan”’s in my life. One was a girl. One was a man who had immigrated from Scandinavia to the US. One was a man who lives and works in Scandinavia. “Jan” (pronounced “Yon”) is apparently a perfectly normal and common man’s name in some parts of the world.
None were confused about whether they were a man or a woman. None of this was a problem at the time for any of them.
And I have known a few women who went by a nickname that was just a shortened version of their name, but that made it sound like a man’s name (such as “Sam” for “Samantha”). None of them were transgender. None of them seemed to worry about it at all.
And offering mental health support for teenagers is a very worthwhile activity.
Personally I would not worry about it.