Coming out as a transsexual isn't something Liv is comfortable with doing yet. Liv sees the way people look down at his non-traditional family (Liv has two mothers).
For Liv, standing up against the dress code is a smaller battle, something manageable. After all, even some girls don't like wearing skirts. So, while Liv works up the courage to come out, Liv can take on the school's rule. But Liv's not entirely correct. Fighting for the right to wear what one wants means putting everything on the line, jeopardizing old friendships and finding new allies.
The book is a busy story with lots of subplots, but an overall message of being yourself and resisting peer pressure. Liv makes a few mistakes along the way, but she demonstrates maturity and generally makes good choices. While Liv's gender identity is an important issue, Clarke wisely puts the topic in the background and focuses the story's drama on the fight over the dress code. It's a paper tiger of an issue but that makes it a cleaner target for the middle reader demographic. And it gets the message across effectively. There is a sense that Liv will prove just as capable at working out who Liv is.