[borninator]

The number of calories are largely irrelevant. The hormones direct what is done with those calories. Is it used or stored. The body has multiple ways of burning more or less energy.

Stating that this isn't a problem if thermodynamics isn't saying thermodynamics isn't real. It is just saying that it doesn't apply in this problem, i.e. it is an irrelevant factor.

It is similar to saying speed isn't the reason you are late to work today. There was an accident and the freeway was locked up. Speed is still real. It just doesn't explain anything.