I thought calories were measured using a calorimeter which burns the food. I'm pretty sure nutritionists don't have armies of volunteers who eat nothing but a single ingredient for 24-hours, whose poop is then burned in a calorimeter to measure the difference?

How much increased absorption are we talking about? If I don't drink a can of Coke containing 150 calories of pure sugar, and instead drink a Diet Coke with basically 0 calories, are you saying that my gut is going to somehow grab 150 calories that it would have otherwise ignored?