Calorie counts are typically adjusted; manufacturers don't typically just toss a bag of, say, Ho-Hos in a bomb calorimeter and use the raw numbers from Igor or whatever recording program happens to be around.

The usual macronutrient values (9kcal/g fat, 5 kcal/g EtOH, 4kcal/g carbs and protein) are surprisingly decently calibrated for metabolic inefficiencies.

They do not, however, take into account hormonal responses, which are probably quite a bit more important than once assumed. So there's that.