Pits are not always straight. If the pit takes a turn to one side before it bottoms out you will only be measuring to the bend, not the entire pit. Pits are a b----- to measure and need to be removed if possible, but do not forget some pits are just benign, some like a cancer and some are hopeless. It is worse with twist or Damascus barrels. The pit will follow the pathway of least resistance and may spread into the layers of metal at different rates and different depths. Each pit needs to be evaluated on its own merits and it is still an educated guess in many cases.