Wait, since one of Chie's defining traits is that she's a tomboy, wouldn't her gender-swapped version have to be a really girly guy?

Genderswaps do not work that way! ...Usually. Generally the artist tries to keep as many identifiable traits intact as possible. In this case, Chie is a tomboy who loves meat, kung-fu, meat, sports, meat, fighting evil, and meat. Thus, she fits the stupid jock type well.

However, that doesn't explain very well why Boy Chie isn't a longhaired prettyboy, albeit a tough one.

I agree. Chie is meant to be unusual for a girl and go against the typical girly things. Therefore male Chie would be unusual for a guy and go against typical male things. The male equivalent of a tomboy isn't a totally regular guy, it's a really girly guy.