I've never been a fan of bike shorts as a fashion choice, especially when combined with a skirt, and it's not for the reasons you're thinking, I feel the same about a hood over a baseball cap and yet it strangely works for Tomo.

Tomo is treated like a bro by Jun for her tomboy personality, an environment in a Karate dojo with a large ham of a Dad can do that, it helps that she is the tallest girl in school and built like a powerhouse to boot but the conflict of the anime revolves around Tomo trying to convince Jun that she is a girl because she has a crush, as early as Episode 2, the subject of her bike shorts gets brought up and she tries a day without the shorts and she barely lasts.
Jun suggests she wears the boys uniform instead but this never happens, which turns her choice of wardrobe into a symbol of her conflicting hormones, the tomboy she's always been fighting against her ever growing love for Jun, it's not as though she can hide her assets either.
It's a common trope that the child who you treated as an equal suddenly grows and you realise they are definitely female or the friend who was your comrade in arms be it a goth, a chad or a sporting teammate is now fully transformed into a beautiful woman. Watamote's Yu Naruse being the best example.
I'm still in an early part of Tomo-Chan, but I am curious to see how this plays out.