Consider the model you're thinking from
This seems to be more of a proof of principle rather than an initial prototype that now needs to be manufactured. From a few minutes of googling and reading (and watching the included video) I see "...method of manipulating at the atomic scale can form the basis for quantum computers, machines that use the effects of quantum mechanics, specifically the spin of electrons around an atom, to represent digital information."
I'm guessing it's the eventual using of the electrons of the atom in question that will represent the data written and stored that defines this "single" atom as a transistor. At this scale "components" seem more defined by function than form. Consider that an atom isn't a single object but composed of many many many subatomic components and maybe someday will count for a number of components within a device while remaining just a "single" atom. Imagine when we can incorporate all the subatomic structures and energies within an atom into our devices.
Obviously a single atom is just an element and by itself can't do anything other then just be that element in relationship with the environment around it. When the atom can be placed very precisely, that placement in itself is information, structure, and organization. Think about it some more and lighten up a bit.
