It's an issue of definitions. Of course you cannot build an electronic device using only a single atom, because you need leads, interconnects, power supplies, measurement equipment etc. So when you talk about a single atom transistor, what's meant is that the critical, behaviour determining region of the device is a single atom. If you took that single atom away, you would not have a transistor any more.

In much the same way we talk about 32nm transistors in computer chips for example - it's understood that this number refers to the gate length, not your whole processor.