This is my first read-through, but it looks as if when Najimi was moving around so often that they became childhood friends with the bulk of Japan, they switched which gender they presented as each time, or possibly even more frequently than that — so it's not that Najimi was presenting as male in Jr High and female in elementary school, it's that they were presenting as the same gender as the one(s) they were childhood-friend-ing.
In the end, it's probably best to consider them nonbinary — the author's probably never going to resolve their assigned-at-birth gender, and certainly won't be depicting their genitalia.