Sure it's a bit more complicated, and it's a fire that doesn't burn 100% of all different fuels. But it's still thermodynamics, but with byproducts that "waste" some macros more than others, which is good if you want to keep your weight down. Edit: And all the second order effects of hormonal/hunger changes.
Sure, physics doesn't stop working. My argument is, are you sure the "its only physics" people are modeling the world in a correct, precise way and there aren't other factors to be considered beyond what they propose.
The point I think the author is making isn't 'calorie counting is wrong' -- 'calorie counting is not the whole picture'. When someone says software is just 1s and 0s, How hard can building software be? You're right its 1s and 0s, but that's not an entirely helpful model to work with if you're trying to build software.
For example, you could say the number of people coming out of a building will equal the number of people that go into a building, its basic Maths - counting is the only thing you need. Now if the person uses this logic for a maternity hospital and they suddenly find out there are more people coming out than are going in. It doesn't mean that math is broken.
Physics doesn't stop working in humans.