I feel like there's a whole subgenre built around girls who are rough around the edges but secretly gorgeous, and sometimes it's done really well. 'Ouran High School Host Club' instantly jumps to mind because Haruhi isn't even trying to be pretty, she's just focused on paying off her debt, and her natural looks completely upend the rich-kid social order. She's smart, practical, and totally unfazed by the boys' antics. It's more about her character than her appearance, which makes the moments when others notice her beauty feel earned.
Another classic is Revy from 'Black Lagoon'. She's the definition of a tough, chain-smoking, gun-toting tomboy in a criminal port city. The series doesn't shy away from her rough exterior and violent skills, but there are definitely frames where her fierce beauty shines through, especially in quieter, more intense moments. She's not conventionally 'cute,' but the artistry makes her striking.