Well,that was sort of the point behind my question. The OP suggested that "time is movement". It's not a big step to say that "time is change". So while you could say, as you do, that time flows for an atom, you support that case by showing that it eventually changes. But you could invert that, couldn't you, that and say that time is change?
And of course the interesting thing, for an single atom, is that its stable state is non-aging - you can't say, well, it's had a long time doing nothing, it's probably going to do something soon.