Sometimes you don't need to rule everything else out to be confident in a diagnosis.

In this case it’s more “when all you have is a hammer (fluoride)…”

The therapy appears to be improving her teeth. Is there something I am missing?

Just because a treatment works doesn't mean it's the best treatment, or is treating the "cause." To say that a lack of fluoride is the cause of their bad teeth is silly. Not eating sugar/acidic foods, Novamin, or a different set of bacteria in her mouth would also improve her teeth.

We used a toothpaste with novamin in it. That didn't help her. She doesn't eat much sugar. She's 40 something kg and eats very healthy.