Everyone is banking on the thermal effect of food, the timing, and the hormonal response from it in the calories do not matter debate.
This is worthless for the following reasons:
Thermal effect: This is useless because it varies from person to person. Either way, carbs are your glycogen, the body's preferred energy source. Ever try to workout in ketosis? Sucks doesn't it? Ever gain muscle in ketosis? Me either. Fat is easily digested, and protein does have a thermal effect, but so does celery.
Timing: Studies show that protein following exercise increases anabolism. How much protein is yet to be determined, however if you can only use so much, it stands to reason anything past that amount is transferred into fuel or stored as fat. The other argument, taking too much of everything at one time causes stored fat: true to a point. However taking less at other times creates the balance for fat loss.
Hormonal response: Take your blood sugar after eating 500 calories of HFCS and then again after drinking 500 calories of whey isolate. Big difference? Didn't think so. Why would the body jack up insulin so much after ingesting carbs, even if it is only a few points higher? Glycogen replenishment and storage right? Why store it? Oh yeah, so you can use it. Insulin is not the enemy, if the low carb crowd had it their way, the body would never release it or at least release very small amounts of it, thus making muscle growth impossible. Plus, it is possible to gain weight in ketosis if you try hard enough, it just won't be muscle and you will look and feel like shit.
Get enough of everything, carbs, pro, fat. Train hard but smart. Rest. Take drugs and/or supplements found OUTSIDE your diet in order to make things work better. Repeat.
Hope this helps.