I don't get the base behind these kinds of manga, tomboys are tomboys for a reason and if they wanted to dress up cute, they would dress up cute. Sometimes you just need to do what you want to do without thinking about what people think about you.
I think in regards to this particular one-shot, it's more that Yoshii seems to feel she has to keep up her image of being a cool chick, whether it's because of her looks or who knows, maybe she was athletic as a kid and it just became almost expected. Peer pressure, if you will.
Totally agree with your last sentence, though.
Yeah, this story has been done before, but this one was done really well, s'cute. Speaking as a lifelong tomboy who enjoys all things cute but would never wear anything cute (although, is matching your shoes with your shirts cute?), I personally never get offended by this kind of story. Not sure why every label we put on stuff has to be so stringent. She can be tomboyish and also cute, why not. Just as Toda can be cute but also kinda cool. That's what I took from the story, anyway.