Nice article but it doesn't really prove that calories are not equal. The article discusses how the calories get absorbed differently, but that doesn't mean the calories have changed or disappeared. Kind of misleading title.
I suppose it depends on whether you're interested in the amount of energy contained in a food or the amount of energy a human being can obtain from the food. We're typically only interested in the latter.
Calories are not interchangeable if you're interested in nutrition (as opposed to burning things).
There are loads of examples, that's a very good one (fibre burns in calorimeters so can throw calorie counts off a lot).
Raw food delivers fewer (usable) calories than cooked food, whether it's vegetables or steak.
Highly processed foods, especially carbohydrates, deliver their calories fast, spiking blood sugar and stimulating insulin production to lay the excess energy down as fat. If you're hibernating for winter, you want the fat. But if you're running a marathon you want slow (protein and fat) and slower (complex carbohydrates) release foods.
Chill your potatoes/rice/pasta for 24 hours and it will have more complex carbohydrates than it did when freshly cooked. Reheat them and they'll have even more. Jury still out on whether this means frozen chips (fries) are a healthy food...
Even the amount you chew affects the number of calories available (analogous to the amount of pre-processing being important).
In this context, calories not being same does not mean there are different kinds of calories.
However calorie source could mean how it's absorbed by your body may differ. So 100 calorie chocolate may provide your body 90 calories of energy, but 100 calorie lentil could provide your body 80calories worth of energy.