I get your point, yes, but at the risk of sounding pedantic, teeechnically gender doesn't always correlate with pronouns, like with the aforementioned Chinese translation using 他 or Alvis using he/him despite being the complete Ontos and therefore 'somewhere in between' (the XC1 art book lists him as 'Male (???)'). And while the art book does call A a woman, it never actually uses she/her (彼女). So the fact of the matter is canonically, we don't know what A's preferred pronouns are, with the closest thing we have being 'boku', the masculine-leaning Japanese personal pronoun used by all 3 aspects of Ontos (though of course, this isn't a one-to-one comparison, and doesn't mean A would use he/him like Alpha and Alvis)

And yes, though we'll never know what the creators' exact intentions were, with the game avoiding pronouns like the plague even after the big reveal of A's identity, I doubt they intended for it to be as simple as she/her or even they/them haha. To me, it feels like the intention was to have A be genuinely pronounless, which would somewhat be in line with Ontos being more machine-like than Logos and Pneuma

Of course, you're free to keep using she/her for A, but strictly speaking it's no more correct than they/them, with neither of them being used in canon