So the article does have some valid points that differences in digestion efficiency, individual calorie expenditure or inaccuracies in listed nutrients, etc. could be sources of inaccuracy when planning your diet. However, what the average overweight person will take away from this is: Counting calories is useless, I might as well just give up.
Having been raised by a very obese mother, I know this attitude all too well. I too, was overweight and desired to keep my weight down and also believed that calorie restriction would mess up your metabolism and eventually make you even fatter.
Eventually, I challenged myself to stop eating sugar since I have a family history of diabetes, and luckily found that I was able to break through my previous sticking point. This inspired me to try to add a little more rigor into my routine, which eventually paid off big time. Now I'm lean and muscular and go to the gym regularly. I find that calorie counting with a food scale is VERY effective.
So I tend to find the fatalistic attitude people have regarding weight loss to be very destructive, not only to themselves and others.