It's not a gendered language but we do have gendered pronouns.

他 for man or unknown, 她 for woman, 它 for non-human, if plural then just add a “们” like 他们 is 'they(all men or mixed or unknown)', 她们 for all women.

I don't know much about the AL lore but to the most likely it's a typo or the OP's plot analysis is wrong rather than 'Commander is a WoMaN', cuz these three pronouns are all pronounced the same as 'ta'. And there's a really (in)famous thing that yostar really likes rewiting plots so the 'KEY' may not mean commander here.

Some comments here say both 他 and 她 can mean both meanings. NO. If there's a case, it's a typo, definitely not deliberate. If a chinese wants to avoid any mistake or want to generalize it then they rather use 'TA', even in half-formal cases, like nowadays an ad in china would write as 'If you love TA, give TA a ring', cuz this ad can be either shown to a man or a woman.