My understanding is that the single-atom transistors is either on or off, no in-between; it can't be used for analog signal amplification.
Amplification does not require linearity in the output. (that's why some amplifiers are referred to specifically as "linear amplifiers", because those
are linear) A relay is an excellent example of an amplifier with a non-linear/digital output. When a small current is passed across its coil, the armature moves and closes a contact that can pass a large amount of current. This is current amplification, where once a small threshold of current input is reached, results in a large change in output current. (from none to some fixed large amount) Basic computers like ENIAC were made with relays and also tubes that were also working in analog (not linear) mode.
This is important in computing because you need two basic functions for computation:
1) a single input must be able to trigger more than one output in the same manner (a different interpretation of "amplification", ten people all chanting your words together instead of one person yelling them out much louder)
2) there must be a way to compare ("mix") at least two inputs to arrive at a variable output. one example is an "and gate", that produces a 1 when BOTH inputs are 1, otherwise producing 0.
neither of these require linear amplification. thus transistors used in computing do not require linear amplification.
But then I suppose I'm straying a little off-topic.