As someone who is not transgender, my opinion isn't worth much. However, looking at it from a biological (not sociological or psychological) angle -

My read is the "nunh" title is a biological role - breeding male, not necessarily a leader or anything. There is a difference between being biologically male and having a male identity; presumably a transgender woman could still become nunh because that's about siring offspring, not being the leader or identifying as male.

Conversely, a transgender male could not be nunh because he would not be equipped for the role. There are two qualifications, and he hasn't got one of them.

Granted, as a fantasy game that has not dealt much with monoracial Miqo'te societies, who knows. Magic is a thing, but gender reassignment options (other than Fantasia, which is a sort of canon thing) haven't been explored since they are not a focus of the plot and it's never been an issue NPCs angst over. More diverse gender identities are acknowledged in-universe (Enuo is only ever referred to with gender neutral "them" pronouns, for the most recent example) but this specific issue with Miqo'te has not been addressed; until it is (if ever it is) I say just follow your headcanon.