Real life isn't a fictional story you read in a book or a quest in a video game. Even textbooks that depict historical context come from different times, regions, and demographics. That is why I used my own experience in this regard. Now I totally understand what you're saying when it comes to men embracing femininity, and females embracing masculinity. The issue in the current time is females rejecting their femininity, and males rejecting their masculinity. These traits are considered toxic when displayed by the sex that corresponds to them, and celebrated when the opposite sex exhibits them. All under a false pretense that this 'empowers' the person, when it does just the opposite. Civilization was not built or sustained by these principles. Our species also cannot propagate in this manner either.
You're right. Not everyone fits perfectly into a mold defined by their biological sex. Ronda Rousy is a great example of a woman exhibiting masculine traits who still embraced her femininity and allowed it to empower her. While Prince is a great example of a man who was very effeminate, yet drew upon his masculine energy to build an empire and a legacy that will exist for decades, if not longer. These two people are entertainers though. Their lives are not what the majority of us small folk go through. Reality bites, it stings, and is often unpleasant. Which is why if you're a woman and someone calls you "handsome" they are very likely making fun of you.
The word "beautiful" is not the same as handsome. It has many different connotations and meaning behind it. The word can be used to describe a sunset, freshly fallen snow, or the birth of a child. The word "handsome" has far more specificity tied to it.
Zero being called handsome would suggest that she looks more masculine than feminine. The antonym to the word handsome you're looking for is "pretty". When a male is referred to as pretty, it suggests that his appearance is more feminine. If Zero was a male, I think the word "pretty" would apply quite well; as does the word "handsome" for her currently. Because Zero has an androgynous look to her, it is easier for both terms to apply to her. My personal take on her is that she still leans ever so slightly towards feminine, which is why I would not refer to her as handsome.