"your body isn't absorbing every calorie you put into it. Your body absorbs until it has what it needs"
Consider what happens if a lactose-intolerant person drinks a glass or two of milk: about 25 g of carbohydrates that their body can't absorb. It will lead to flatulence and diarrhea as a result of gut bacteria feasting on those unused calories and the inability of the body to extract water effectively from a sugar solution.
The fact that this is an abnormal response shows that the normal thing is to absorb every calorie.