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.