I'm really surprised nobody in this thread brought up the very clear and intentional trans subtext in this manga because it feels so obvious to me.
The topic is brought up explicitly with the "pre-op transexual" line, which Chihiro does not refute but instead says "You're really rude!", which is accurate: don't go speculating about someone's genitals or medical history, people.
The subject of the theme is made obvious when Chihiro describes her childhood, saying "everyone mistook me for a boy when I was young, so I couldn't ask for girly things from my parents". This statement could only really mean two things and the non trans explanation (she was an only child raised as a boy by a family who really wanted a son) is a huge reach, because it makes the "so" of that sentence and the "A therefore B" structure it indicates not make sense.
Finally, the theme comes together with the plot as Chihiro marks her successful journey to self acceptance and confidence in fully embracing who she is by changing the main character of her semi-autobiographical novel from a man to a woman.
And if all that wasn't enough, she's even got a puppygirl gf, like that alone should convince anyone :P
This trans theme enhances a few different scenes of the manga: Nagi being the first person to intuit Chihiro is a girl, the manager being wishy washy in pursuing Chihiro, and Chihiro in the ending presenting much more femininely, including having a more curvy body.
And sure, you COULD argue against all of this... but nobody actually likes the "that thing you think has meaning is actually meaningless" argument, it's just a thought terminating conversation ender ;)