Well, I'm not twisting the physiology of it. That's how it happens in a P+F+C scenario. It's basic stuff.
There are plenty of studies that show how various meals made up of P+F+C combinations are deleterious because of their macronutrient composition. This implies that P+F and P+C combinations are less deleterious--in the short-term at least.
However, eating clean in MANY individuals may have positive effects that outweigh those of Berardi's meal combination rules. But remember, this has a lot to do with what happens hormonally BETWEEN meals, when insulin is down and glucagon is up.
Let's look at 2 hypothetical individuals after the same P+F+C meal containing 35 grams of clean carbs and 120 calories of fat. 3 hours later, Individual#1 may have got back into significant lipolysis. Invididual#2 may have ZIP lipolysis.
If these postprandial responses are typical, and the macronutrient breakdown of the meal reflects their diets, then Individual#1 will tend to accrue less bodyfat on either a bulking or a maintenance diet. He'll also burn less muscle on a cutting diet. Individual#2 will accrue mroe bodyfat when bulking, may very gradually put on bodyfat while on maintenance, and lose more muscle when cutting.
In the case of Individual#2, he may do better separating his carbs and fats. Something Berardi doesn't go into much is techniques to deal with the transition between meals that contain lots of carbs and those which contain lots of fat. This will also help Individual#2 in all his goals.