How we measure the calorific value of food doesn't seem to give us the number of calories a body can extract from food.

There are several reasons for this. One promising area of research is gut flora. Someone could have a gut flora that makes it harder to absorb calories. Someone else could have a gut flora that makes it easier to absorb calories.

Here's one paper that links gut flora to anorexia. (Read carefully, they have human samples buried in there) http://www.nature.com/tp/journal/v4/n10/full/tp201498a.html

> Statements like these only help people who have weight-problems to have an excuse not to do anything about it.

No. Statements like this are an effort to help fat people to lose weight by creating treatments that work rather than just yelling judgemental but useless advice at them. "Eat less food" does not work on populations. "Exercise more" does not work across populations.