I'm not sure that is true. However, I admit that I know little about nutritional science. I am a physicist by training, and from that point of view, it is possible that different amounts of energy are required to release the energy stored in the different types of food. The total energy available in a theoretical sense would be the Gibbs free energy. I don't know if nutritionists use combustion or something else when determining the caloric density.
Well, I should have spoke with a little less certainty (not unusual). So I revoke that, apologies. http://www.precisionnutrition.com/digesting-whole-vs-processed-foods Mentions what you are talking about "the cost of extracting energy" if you will. That includes: calories from chewing, cutting, and digesting food through different pathways. This particular article cites proteins as taking around 20-30% of their caloric content, carbs taking 5-10, and fats between 0-3%. That being said, this time I'll qualify this information appropriately, instead of being an ass. Human nutrition is a complicated field, and very VERY expensive to examine appropriately, because of all the variables at play. I should not have said 2000 calories of anything will EXACTLY impact your body in the same way, but I think a revised statement might work. "Within a margin of 30%, any calorie will impact you the same way." You could either adjust your dietary calculations to account of this discrepancy, or, as most people do when they successfully manipulate their intake, just leave a wide enough margin (positive or negative) to absorb those differences and still achieve your desired net goal.
If I'm not mistaken, all those considerations are taken into account when they calculate caloric information on labels. If the package says 100 kcal, that means that eating it will give your body 100 kcal to burn for fuel, build into muscle or store as fat. Obviously if you did something like convert the matter into energy direct by means of nuclear fusion you'd get a hell of a lot more than 100 kcal out of it, but the label is meant to be understood as the amount of net energy the average human body can extraxt from the product. In terms of strictly weight gain and weight loss, a calorie is a calorie. In terms of general nutrition there are other considerations (which basically boil down to: eat lots of vegetables and lean sources of protein, and get your carbs from foods that are high in fiber), but the number on the scale will directly correspond to the number on the nutritional information.