A single atom most definitely cannot have kinetic energy all by itself. SR/GR makes it abundantly clear that you must have something to reference against to make a measurement, and the answer changes depending on which reference point you're using. This should be obvious to anyone who has driven a car. Let's say you have three cars, yourself going 50mph north, a second car ahead of you and to your left going 45mph north, and a third car going 50mph ahead of you headed south. You have to swerve left or right due to an obstacle ahead, which do you choose? Obviously you're going to swerve left, ignoring the velocity of your swerve itself, you're going to overtake the car on your left a a relative 5mph and if you go right you'd be moving 100mph relative. Or you could split the difference and drive directly into the obstacle which is going 50mph relative to you.