The logical conclusion for the characters (and player) to come to at this point is, “Chihiro is a trans girl”.
Keep in mind, up until this point Chihiro has presented entirely female. The characters remark on how she was “really a boy” and instantly switch to describing her with male pronouns for the rest of the game.
During the trial, a second examination of Chihiro’s body reveals she has male genitalia. Let’s start with the chronologically first one. There are two main issues I have with the portrayal of Chihiro.