When I read the FAQ I read it as (and this may be totally wrong but seems like a possible interpretation):

The FDA says we have to say it's not effective on nails and scalp and we can tell you they make us say that so we can't go out on a limb and tell you "…but our product does work on nail fungus" that contradicts what they tell us to say. So the best we can do is tell you that the product is intended to be applied to the skin on the toes and around the toenails and hope that you understand that that means the product is for toenail fungus. The "see your doctor" line is another disclaimer so the FDA doesn't go after us for giving medical advice.

Robert's comment about treating the living cells and waiting for the dead cells, i.e., nails, to be replaced supports that but obviously it's not clear.

Anyway, I hope that's what they mean. From my antifungal experiences, any antifungal medication should just have the disclaimer: "Results from the use of this product are, as always, hit or miss."