Chris makes a number of errors in this article.
1) It's completely misleading to say that "high-fat diets make you fat" when it's not macronutrients, but negative calorie balance that determines weight loss. Calorie balance already takes into account TEF on the energy out side. If you're eating well under maintenance, a diet is not going to make you fat, no matter how much of the diet is fat (or carbs).
2) Excess protein is rarely stored as body fat. Its primary fate is oxidation or gluconeogenesis (conversion to glucose). The pathway for de novo lipogenesis from amino acids plays a negligible role.
3) Leptin is produced by fat. It is doesn't signal fat cells to inhibit lipolysis.
4) The catabolism produced during a skipped meal (or overnight fast) is almost completely offset by increased protein synthesis during the next meal, such that protein balance is largely static. It makes no sense to be talking about a "muscle wasting state which, in turn causes the metabolism to slow." People appear to lose fat and maintain muscle just fine with intermittant fasting and only one big meal per day.
5) He contradicts himself to say that you should eat less later in the day, because of higher glycogen levels, but that it's fiction to avoid carbs at night.
6) He's incorrect to think that glycogen sotres are going to be anywhere near "full" at the end of a day of dieting. Absolutely not. When you're NOT dieting, it takes several days of massive carbohydrate overfeeding to fill up glycogen. Until that point (which is practically never reached, especially on a diet), there is essentially no conversion of carbs to fat. Rather, carbs are oxidized and stored as glycogen.
7) Caffeine is believed to increase metabolic rate primarily by inhibiting the phosphodiesterase-induced degradation of intracellular cAMP (thus increasing cAMP levels). Catecholaminergic stimulation or adenosine antagonism appear appear to play only minor roles.