Estimating wrong how many calories you're consuming & how many you're burning is why the first phase includes keeping track of it--it helps you make good estimates and gives both you and the doctor useful information.
Yup. Also, one thing that I realized when I was losing weight through tracking calories (in and out) was that it didn't really matter if my estimates for intake and burn were off (although I tried to keep them as accurate as possible), so long as they were consistent. If I was weight-stable at a certain number of rjstanford-units of intake and output, then by increasing output while maintaining intake (or whatever) then I'd lose weight. Accuracy vs. precision and all that. Worked pretty well, too (dropped 80 lbs about a decade ago and went from sedentary to IMs).