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Everyone's gender is canonical here (except for the original characters, and Plagg but hold that thought), but where we're apparently supposed to assume everyone in canon is cis, Marinette and Adrien are trans. Marinette is very clearly a girl and people know she's trans even though she doesn't much talk about it (and before she mentions the fact here, nobody knows Ladybug is trans), and Adrien is...closeted. Really aggressively. Everyone knows Chat Noir is a boy, so obviously no one is thinking the profoundly femme Adrienne Agreste might be him.

Plagg is canonically a user of he/him pronouns. Since every kwami we've got pronouns for so far uses pronouns that match their wielder's and (by Word of Astruc, I believe) they're all genderless, my thought is that is a thing kwami generally change to match new wielders, and Plagg thought this one was a girl. Except how the transformation manifests is largely driven by the wielder's idea of how it should, and failing that, by how the wielder wants it. This kid wanted a binder, a cosmetics-free face, and a haircut; well, he's not Plagg's first trans wielder. No point Plagg asking him for a change of pronouns, either, because there's no reason for her to prefer one set over another, and having told this kid to use 'she', telling him to use anything else is a waste of time better spent lazing.