(Calories in - calories out) is correct enough to be the single most reliable metric, and will serve you right 99% of the time. My "one level deeper" understanding is that there are a few transfer functions applied to calories in. So of the technically available calories you eat, how much does your body absorb. Then, when the calories are biologically available, how does your body spend them?
So the idea would be, if you eat the pizza at the right time you reduce calories in. Either you will digest less calories, or your body will allocated them differently at different times of the day.
Unfortunately these things aren't really measurable so it's very hard to separate from hearsay.
It is, but CI\CO as advice doesn't take in to account that you aren't a machine and we aren't calculating gas mileage. The system is both adaptive and reactive. CI and CO changes based on the situation, and you have no way to accurately measure.