It's not about running a caloric deficit, but a caloric restriction. Usually the goal is reducing your caloric intake by 20-40% compared to your regular diet. You don't need to run a deficit and burn more than you take in or you would waste away.
Surely if the human body were a simple machine, as some people argue, then you would be running at a deficit? Any excess energy would have to be stored. In reality, however, the body can adjust to a range of energy input and allow you to run at lower levels of input, albeit with a reduced metabolism.