That has to be at least partially it for the rest of your comment to be right (which it is!). To say the atom was "held nearly motionless" is to say it moved a little during the exposure. It sent the light toward the sensor from all of its positions.
No, not at all. The wavelength of the light is about 1,500 times larger than the atom emitting it. So the atom would need to move at least 1,500 diameters to make any difference in the light.
You can't see single atoms because they normally don't send any light toward you. But if they did, and this one is, you would see that light.
You aren't seeing the atom exactly, you are seeing what it sends toward you, and the human eye can see single photons. (And so can cameras.)