Why doesn't she qualify as a Tomboy for you?
Why would she? Especially as of chapter 1 (but even as of the most current chapter as of me posting this), there's no insight into her interests and how society views both said interests
and the fact that she-- as a woman-- has them. Tomboyishness is normally characterized as "girls doing boy things", but the heart of it is that they engage in behavior that doesn't conform to the given society's sex-based expectations for women (which often means that they do "boy" things more so out of what happens to be the case-- there are only two sexes to have expectations for, so if their interests aren't popular with girls it's likely the case that they're popular with boys). That may happen incidentally-- they're more concerned with their interests than whether they fit sex-based expectations of them as females-- or it can happen on account of some hatred of femininity and/or other women. Perhaps it happens because of an abundance of male influence (e.g. her family is majority male) they happened to take to. As for Nonamoto: one could point to her factory job, but said job's not much characterized (it doesn't matter enough to be) and we also see women working there at any rate.
Her thinking patterns and more general behaviors also don't portray the aforementioned tension of "girl doing boy things" (or "girl
thinking boy things", in this case). Not that she isn't characterized at all, but that the characterization she's received so far doesn't involve the aforementioned.
Even on the most superficial level-- her looks-- she doesn't really fit the stereotype. Her hair's braided, and she puts them up into loops at work. The closest to "tomboy" she gets is that she wears pants, and perhaps that her body is "plain" (but her body shape isn't entirely deliberate on her part-- I'm reaching at this point). I say this is "superficial", but even her appearance can portray her personality: the stereotypical "short hair" and boyish dressing of many tomboys (characters or real people), for example, can be the result of those things being practical for physical work or activity (things seen to be predominantly in the "male" domain) or just "easy" to tend to (a manner of thinking also often ascribed to men). Alternatively, they can be the result of wanting to adhere to either a boyish style-- or at least one not attractive to girls in said society (whether that's deliberate or incidental on the tomboy's part). As far as Nonamoto's been characterized, though, she's a runaway that's been struggling to live paycheck to paycheck-- she doesn't appear to have the luxury of clothing choice, to begin with.
I could turn out to be wrong as her character is further developed. Currently, I'm of the mind that both her design and (secondarily) her character are the product of the mangaka wanting a female protagonist while also wanting to suppress potential sex appeal.