The proposed control algorithm is simple: when eating a meal, eat a total weight of food and drink (F(t)) that is the weight you would like to be at the end of the meal (r(t+T)), minus your weight at the start of the meal (w(t)). This rule ignores metabolism, so you will fall below your target weight by the next meal, but you will eat accordingly more then.
Obviously, as the article notes, this requires that "the reference r(⋅) has to be chosen larger than w(⋅) at all times". You can see this in Figure 1: the measured mass starts below the reference, then increases up to the reference, then falls below it, then increases up to it at the end of each meal.
Not, strictly speaking, true: not only must we consider mass-energy equivalence (the chemicals bonds in food vs metabolic byproducts could contribute unequally to mass), but more importantly, we inhale mass well as ingest. From the article, one mass-unit of inhaled oxygen produces less than one unit of exhaled carbon dioxide (although I suspect that more than enough water is lost though net exhalation alone to make up for it). So we have to be a little careful with this conservation of mass argument. It's still basically correct, though, and more-or-less blows the "weight gain is exactly proportional to excess calories" argument out of the water.