Scientifically sound food recommendations [1] accept that different types of calories make you feel more or less full."
That's a contradiction. The entire idea of "calories in, calories out" is precisely that there is no difference and all calories are exactly the same. If some make you feel less full than others, then you're invoking the existence of the feedback loop that "calories in, calories out" explicitly denies.
If you, as this article does, point out that many things affect whether a calorie can be absorbed, that is, again, another difference between calories.
If modern science is moving on... and it is, at an inexcusably sluggish pace... it's moving on from "calories in, calories out". There's really no way to salvage it... even if you want to go with "calories digested vs. expended" you've still got a complicated feedback loop even there between the pancreas, insulin, blood stream, various bits of the brain, the metabolic consumers of blood sugar (significant differences here too between muscles vs. organs), etc, and even two people who hypothetically start with the exact same blood sugar levels and digestive system state will rapidly diverge as this feedback loop does different things between them. "Calories in, calories out" is only true as a limit on the system of the bodies, it isn't even remotely suitable for use as "the only parameter in a model, which gets set to a constant value". (What other bodily function works so simply? What makes digestion so bizzarely unique that it can be modeled so simply? None and nothing.)
(And a rather pointless limit in some ways, too... nobody is running around claiming that the human digestive system is an over-unity perpetual motion machine, so making such a big deal about thermodynamic limits is rather silly.)