Two reasons why:
1.) The bottom of the tank is shaped such that there is a shallow end and a deep end (like a swimming pool), so the lower half of the tank simply contains less volume of fuel than the upper half.
2.) The "flower pot" displaces some volume and returned fuel is mostly retained within the "flower pot" during vehicle operation to provide a steady supply of fuel to the pump, rather than being returned directly to the volume of fuel outside the flower pot. During vehicle operation at extremely low fuel levels the level of fuel within the "flower pot" may be quite a bit higher than the level of fuel remaining outside the "flower pot." Thus the lower register of the fuel gauge may read just a little lower still after a few minutes of fuel circulation than when the ignition is first switched on. This also explains the anomaly of the red low fuel level light being dark when first turning on the ignition, and then illuminating a few moments later even though the engine was not started!
