There isn't "much data" being stored on one atom, there is one bit. For each additional bit stored, another atom is required. What is changed/controlled is the spin of the atomic nucleus, which can be "flipped" by an rf pulse.
Right, when they say data on an atom what they are saying is that they can detect a toggle. Which means they can store a 1 or a 0 on an atom.
And there is the fallacy in reporting that you can store 1 bit in 1 atom. The overhead needed to address each individual atom among quintillions, apply the pulse while not affecting other atoms, and later read it out likely requires at least tens of thousands of atoms for each data-storage atom. So while this is cute, it is subject to the law of diminishing returns once you try to make it into a product.