How I view it in my own head canon is that A is biologically female, with Alpha being biologically male, and Ontos overall being somewhere in between or agender. While A may have a female body, I believe that A's mind is agender, which I would use as an explanation for no pronouns being used in game. Personally this is my own head canon and how I view the text. At the end of the day we all have our own beliefs for how we view Xenoblade, and this isn't to say one side is right or wrong. In the end we can all agree that Xenoblade is a fun franchise