I ran 16 miles this morning, burned over 2000 calories. But I won't lose any weight, I am going to eat those calories right back.
In a thought experiment (where it's possible to know the exact amounts) -- do you think consuming exactly 2k kcal is perfectly even with burning exactly 2k kcal? IE, is there overhead to transform the energy? Does it account for physical/energy waste?
The energy expenditure does account for waste, I think only about 20-25% of the energy spent is turned into mechanical output
You might enjoy this: http://theoatmeal.com/comics/running