Punishment presumably doesn't work for thoughts, because it rewards the negative of the thought in the same movement. I expect that it's rather switching to procrastination that is rewarded, not continuing on the task that's punished. The behavior here is not static "thinking a thought", but rather a transition between possible thoughts.

The longer you try to concentrate on the task, the more willpower you apply to it, the more rewarding the behavior of switching the attention to procrastination becomes. And so, you learn to do it automatically, thinking of nothing else whenever you start thinking of getting the work done.