I haven't read the whole book, so I'm just going off of Berardi's articles where he writes about this type of nutrition program. In the articles he states that these formulas are merely an estimated amount of calories. Some people need more, some less.
In his Massive Eating Reloaded articles, he talks about slowly increasing calories over a period of weeks, until finally you settle on the right amount for your body, gaining weight, but hopefully not too much fat.
Massive Eating Reloaded, Part I
I'm surprised that it's not in the book, too.