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For a start there isn't a problem with "tomboy" characters any more than there is a problem with "reluctant hero", "girly heroine", "goofy side kick", "wise old man", “small, cute yet unidentifiable creature”, "evil villain" etc- they are all standard characters in anime & manga.

If you need to explain why someone is a tomboy then that is a different question. Tomboys may be because a girl has grown up; without a female road model; with lots of friends who are boys; with lots of older brothers; hiding their identity due to trauma; who are gay (if you want to follow the strong\ girly lesbian role model); who exist in a tough environment ...... list goes on and on.

If I can give you some advice when writing a story, you need to ask one question over and over- what is this character’s motivation? And a lot of motivation will come from back story, so make sure you understand why someone is as they are, by thinking about how they have lived their life, otherwise you end up with shallow characters. “Flashback” is your best friend in this situation.