Charlotte Doyle is a girl who dresses as a boy. From this we can assume that this novel wants us to think about gender and what it means to bend it, shape it, any way you want it. For example, Charlotte wears a dress around her family and becomes quite feminine, but on the boat, she puts on canvas trousers and becomes masculine. (They even start calling her "Mister," right?) Charlotte's gender can vary depending on the situation. It's malleable, like Silly Putty. If we were feeling particularly academic, we might even say that Charlotte's gender is socially constructed. (Yes, we're pushing our glasses up our nose right now.) Also note that Charlotte's ever-shifting gender is often contrasted with something that does not change: her biological sex. Though she wears boy's clothing, she always keeps her girl's body.
By changing her gender, Charlotte paves the way for radical shifts aboard the ship.
Charlotte may be able to switch genders, but she'll always be a girl. The amount of change she can enact is therefore pretty limited.