It corresponds to the value of the unimproved land. So the tax paid by a skyscraper would be roughly the same as that paid by an empty lot of the same size next to it. (You can imagine a system where a tall building would have to pay more tax for blocking out the shared light).

If the burden of the tax were shared equally than the penthouse would contribute the same amount as each of the floors below it—some small fraction of the total for a tall building.