This is kind of a thorny problem to solve. There are only two ways the software can learn the user’s gender: (1) adding a field to the sign up page and (2) adding a field to the profile.
If the solution is (1)… I’d be totally against this just on the conviction that sign up pages should have as few fields as possible. Even if you don’t care about the length of the signup page, asking gender to new members seems kinda weird. You are likely to offend more people through asking their gender at signup than through using a masculine grammatical form in some languages.
If the solution is (2)… The ship has probably already sailed on using the correct gender. Here on Meta, less than 5% have filled out any profile information. I would guess most people who take time to fill out the profile page have used the service long enough to receive most of the system messages such as “You’re now certified.”
I agree that gender neutrality is a great idea, but I doubt there is presently any good way to implement it in discourse at present. There simply isn’t a good method to learn a significant percentage of the users’ genders early enough.
You could, however, translate around this problem. You could ask translators to use gender inclusive language in their translations through means such as avoiding the second person in languages that mark second person personal pronouns with gender.