@alanala
Fair point, there has been cases where female characters use masculine pronouns (regardless if they were hiding their sex or not).
I don't believe people in Edo are generally or in the majority sexist, I see the gramps as in the minority because I have only see him act sexist (and even then it's only regarding his ninjutsu) and no one else shares his sentiment. Although the only female warrior/soldier in the bug magistrate is Hibachi (so far), she has either been treated amicably or neutrally by most of the population in Edo.
That doesn't mean it shuts down the theory that he/she is hiding her sex/gender identity. Perhaps where Chiyomaru came from, female warriors are looked down upon/forbidden, or perhaps Chiyomaru prefers to have a male gender, or maybe even because Chiyomaru finds it funny when people find out about his/her real sex/gender. Anything can happen really, since we don't know much about Chiyomaru.