I have no idea what Eliezer would think on the subject.

Allow me to enlighten you.

My feeling is that if a metamorphamagus is changing the body, then this means changing the hormones-- they're a member of the sex they appear to be in every way with the possible exception of childhood memories. (I don't remember at what age the ability to metamorphize kicks in.)

Well, that depends on how said hormones are affecting brain development during childhood and in the womb - and I don't recall hearing tales of transsexuals taking such hormones having, say, their sexual orientation affected. (I haven't researched this.)

On the other hand, there's mention in canon of a baby changing their hair color, which would indicate that it doesn't "kick in" at a specific point in time. I'm not sure what this means for the gender-changing-Tonks hypothesis; is there any research into children with irregular levels of sex hormones, or who started taking hormones in childhood?

I could argue that that they're "really" a gender we don't have a word for.

Androgynous? Hermaphrodite? Genderqueer? Those are words, and while their meanings are ... fluid ... they could all probably be applied to such an individual.

Ultimately, we can never be entirely certain one way or the other without Word of God; magic can cover a multitude of sins. Unless his opinions have changed since he wrote that article, however, I'm guessing the most she could achieve would be an inferior "penis-shaped vagina", perhaps with looks based on a specific individual for realism. If her powers actually bother dealing with hormone levels and such, it's presumably dealt with automatically, so it could simply refuse to mess with sex hormones beyond certain limits. She carried a baby to term in canon, and there was certainly no mention of having to avoid certain transformations. Not that there would be, necessarily.