It's just a misunderstanding of what calories in and out refer to. Most people think the calories in is the calorie content in the food you consume, when in fact, it is the calories of the food you consume MINUS the calories that are not absorbed and the calories spent in the absorption process. Therefore 100kcal consumption of sugar is not the same as 100kcal consumption of meat, since the sugar is easier to absorb, meaning the calories out is smaller, ie the effective calories in is higher for sugar than meat.  So it's more complex than calories eaten ("in") vs calories out, but the governing law is still calories into the system vs calories out of the system.