The type of food is what makes a difference. Fatty foods are worse than the same caloric-quantity of fibrous foods (i.e., fruits and veggies).
And there's plenty of research to suggest that food in - food burned by activity (inc. exercise) - undigestable food = food stored as fat.
Do you know how the magical "1g protein = 4kcal, 1g carbohydrate = 4kcal, 1g fat = 9kcal" numbers were reached? Hint: They were never measured in vivo, or in vitro cells -- the follow from a very fragile theory, which breaks in every way you look at it -- and yet, it's considered "science.
I thought his theory was about tricking the body with taste-free calories in order to dampen hunger pangs. If so it fits neatly within that theory since less hunger means less eating means less calories.
In fact since it's billed as an "eat anything" diet, doesn't it contradict Taubes who targets refined carbs as the real villain?
You should read the things I've referenced.