A chain of links lead to a Scientific American blog post about digestion. Processing food makes it easier to digest (which is part of the purpose of processing).
In general, it seems that the more processed foods are the more they actually give us the number of calories we see on the box, bag or other sort of label. This applies not just to cooking and pounding but also to industrial processing. A recent study found that individual humans who ate, as part of an experiment, 600 or 800 calorie portions of whole wheat bread (with nuts and seeds on it) and cheddar cheese actually expended twice as much energy, yes twice, in digesting that food as did individuals who consumed the same quantity of white bread and "processed cheese product." As a consequence, the net number of calories the whole food eaters received was ten percent less than the number received by the processed food eaters (because they spent some of their calories during digestion).
Interesting. And people and their responses vary too--though I'd love to know where the author got this tidbit:
Back when it was the craze to measure such variety European scientists discovered that Russian intestines are about five feet longer than those of, say, Italians. This means that those Russians eating the same amount of food as the Italians likely get more out of it. Just why the Russians had (or have) longer intestines is an open question.
And of course there's a lot of variation in gut bacteria do a lot of the heavy lifting when you digest food. Hmm. How many antibiotics did you have to take, and what other effects did they have?
So there's no substitute for carefully monitoring how food, exercise, etc effects you, trying to control one variable at a time. The problem is there are so many variables: time of day, amount of exercise, variety of foods ...