Later in the game, The Fractured but Whole asks you to choose your character's gender. In a conversation with South Park school counsellor Mr Mackey (the "drugs are bad MKAY" guy), you must choose from three options: male, female and other. In previous South Park game A Stick of Truth, you had to play as a boy.
It turns out, if you pick a non-male character, Ubisoft will use the conversation with Mr Mackey as a smart retconning of The Stick of Truth.
"So the whole King and Stick of Truth thing, she was actually a girl the entire time?"
Mr Mackey then asks you to clarify exactly what you mean by a girl. You're then asked to select whether you identify as cisgender or transgender.