I'm pretty sure the way calories are measured is using a calorimeter. There's no correction for the ability of our body to absorb calories from a particular food, because 1) it would be really subjective and controversial and 2) the junk food industry would go bonkers over it.

Here's how the FDA site defines it: Calories — on the Nutrition Facts label are the measure (amount) of energy in a serving of food. For example, there are about 110 calories in 1 cup (8 fluid ounces) of orange juice.

Note that they describe it as the "energy in a serving"... not the "energy absorbed from a serving." The measure is independent of our body's ability to extract that energy, which can vary wildly.