Yes, it is entirely normal for 1 to 2.5 cm of water to remain in the upper and lower chambers. For water to be filtered, it must pass through very fine micropores in the filters. The lower the water level in the upper chamber, the lower the pressure available to force the water through the micropores. You may have noticed that the filtration rate is much faster when the upper chamber is full than when it is half empty. This is because there is more pressure. The only way to remedy this would be to enlarge the pores of the filter elements, which would reduce the effectiveness of the Berkey purification system. During each cycle, the residual water from the previous cycle mixes with the water from the current cycle and is then purified. Therefore, there is no need to worry about the excess water during normal use. However, if you stop using your filter for an extended period, such as during a vacation, it is best to empty both chambers and let them dry completely.
Regarding the lower chamber, the spigot cannot technically be positioned at the bottom of the tank for sealing reasons. Don't worry; this is not stagnant water as it will mix again and again during successive filtrations.