The body isn't a closed thermodynamic system. You have to take into account metabolism, the human waste that is eliminated, the satiety of the foods consumed, etc. Not to mention the make up of bacteria as evidenced in the article.
You're also making the assumption that less fat results in a healthier human being. that is also something that depends entirely on the nutrient content of your food. You can lose weight by eating nothing but small portions of white rice, but it's not going to result in a healthy individual.