I think this must be an artifact of the fuel gauge used in this specific car. In the Prius i have never noted any of this effect. Thinking scientifically:

1) the pressure added by the fuel pump is probably orders of magnitude higher than the small pressure difference caused by the lower/higher level of the tank
2) Newton says that it requires more energy to accellerate a car with a full tank than a car with an empty tank, i see no room for FE improvement here
3) You need to measure over long periods to make any claims, so fill the tank, drive for two gallons and fill her up, calculate the FE. Then allmost empty the tank, and fill her up with 2 gallons, do this for 20 times and compare the difference.
4) People who allways fill up and then empty the tank tend to make fewer visits to the station, thus improving "usefull" milage (relativly less gets wasted during the visits)