In the case of this particular story (which had those responses when I posted it at FF.net), Ao3 allowed me to label my fic in ways that showed that I considered all the relationships in the story het (by labeling it M/F only instead of both M/F and M/M). Saying the same thing explicitly on FF.net would require a textual author's note.

So, while it wouldn't stop someone from referring to my story as "yaoi" (having m/m content), it makes clear that I, as the author, think of all relationships in the story as being het (there's background implications that the cis man is interested in another cis woman).

Freeform tags (such as 'transgender' or 'transgendered character') would also say that I am interpreting this character as being transgendered (this character in canon has been labeled as being both 'transgendered' and 'transvestite'). In addition I've written other stories with her with labels like "women being awesome" and "female friendship"

So in other words, not only do I use the feminine pronouns in the story, but Ao3 has more ways of signaling at an extra-textual level that I mean for this character to be interpreted as a woman.