@Caid
Don't forget many of these asian languages
do have the equivalent of gender neutral pronouns. Translators tend to insert he or she based on assumptions in the story or their own biases. So we can't say for sure they are referring to whoever as any particular gender unless you can read the original language and have access to the raws.
Secondly it's irrelevant if characters refer to the MC as male or not, they have no way to know. Their random assumptions are meaningless. They assumed that female fighter was male solely from being a fighter in armor for example.
Lastly, it's good to have gender neutral pronouns for English, so I sincerely am curious as to what is most acceptable and understandable for the average English speaker. And to have one, not many to suit unique circumstances.
The MC skeleton is a person, has sentience. Would you want people to say it in reference to you if there was a circumstance where your gender was unknown? And that circumstance is now even since I don't know your gender. But no need to tell me, just tell me what gender neutral pronoun you'd prefer to use for you with us not knowing. I assume you would not like to be called an "it" and I have a relative that considers themselves as the other gender and has definitely told me that "it" was unacceptable.