My mother taught me to change tires, run chainsaws, and operate heavy machinery.
One of my best and only friends growing up played sports and she build things in the dirt with me at least as much as she did anything feminine. In fact, her mother sort of dreaded us spending time together because I encouraged her desire to play in all the mucky, shitty, slimy places I did.
I’m not sure I’ve ever heard my mother refer to herself as a tomboy, though she certainly grew up doing things often associated with males, as expected being the eldest child on a large farm. However, my friend did call herself a tomboy, and to the best of my knowledge, it wasn’t a loaded gun pointed at the head of her womanly esteem. She’s actually one of the most well adjusted people I know. While perhaps the two possible pitfalls you list are valid concerns, I don’t really see them present in any of the girls I know who identify as tomboys or who were called that growing up.
i grew up in a family of "tomboys," grew up doing carpentry, changing tires, raising dogs, and horses etc, etc... and being called a tomboy the entire time. my mother still calls me a tomboy.
and i have trouble with women. because, while being called a tomboy, i was being praised for being apt at anything mechanical, and hearing that my great grandmother was, to quote my grandmother, "a ninny," for being feminine, and generally opting out of heavy or complex manual labor.
so it was totally toxic for me, and contributed to the internalized misogyny i later had to process, and overcome, and still sometimes catch myself participating in.
i was also taught by example that men only truly respected women who are "handy." you have to earn having a man listen to you by being tough. that a pretty woman must equate her value with her appearance, and that one who invests herself in indoor pursuits is not to be given the same type of trust a tomboy would, because a tomboy is masculine, and therefore is more logically capable than a "girly girl."
so yeah, my suggestion would be to actually ask your friends, and see if any of them have ever considered the negative implications of the language being used. because i don't talk to my friends about this shit, either, so i'm sure they make the same assumption about me.
but it surely effected how i grew up thinking about men, women, and myself.