The part where you restrict your assessment to more or less normal digestive function? Obviously if your stomach explodes or your intestine just plain stop working, caloric intake/deficit is now one of the least of your worries.
I think you actually hit the nail on the head here though, in using the word "imply". Calories in - Calories out doesn't give you an exact picture, but it comes reasonably close for the purposes of most people.
It's by no means a perfect understanding, but someone who is obese needs simple rules that can successfully get them started more than they need a perfect knowledge of the science involved.