Thank you for sharing an interesting article.
For my purposes, a calorie is a calorie. I think, if you read more about this particular thesis, you will see that there are different ways of assigning calorie content. For instance, some nutritional analyses count the calories in both soluble and insoluble fiber. So we may not know exactly what the calorie count means to our bodies.
People who make comments on articles like this tend to be very passionate in their views. Unless you want to spend the rest of your life doing research, you probably need to take it all with a grain of salt, so to speak.
Only you can know what works for your mind and body. If sweet foods make you have terrible cravings for more sweet stuff, you need to think about what this means to you. If you can't eat just one slice of cheese [talking about me on this one], you need to think about practical solutions to the cheese problem. My solution here is to not buy cheese.
Calorie counting is an imperfect science. Be consistent, honor what works for you, and be honest with yourself and you will do fine.