I would associate N/A more with agender (someone who has no gender) more than someone who has a gender but it is not listed. For me, my gender is applicable, it's just not in that list.
"Not Listed" might be a better title for N/A?
Edit: Just saw your edit, makes more sense. Still feels a little on the edge for me, but we're all going to have different needs out of something like this.
The purpose of the standard is to give a numeric code which is language agnostic, for internationalization of forms and software.
Adding other genders isn't really applicable, since there's no common meaning or terminology across languages. M and F are universally recognized because they're grounded in reality: Every language in the world has a term for them.
"Not Listed" might be a better title for N/A?
Edit: Just saw your edit, makes more sense. Still feels a little on the edge for me, but we're all going to have different needs out of something like this.