There is a reason it suggests to eat them back, which is entirely logical. Basically, the notion is that you should never eat less than your BMR, which for most overweight people will be much higher than 1200 cal.
There is a great method for working out how many calories you should be eating that doesn't involve 'eating back' the calories you exercise, but allows you to eat a healthy amount of calories and still lose weight just as effectively.

There is a fantastic thread on the MFP website about it, if you are interested.

Anyway, it does make sense, it is just a different formula and method to a strict VLCD, which is what 12WBT essentially is.