I bought this toilet but do not understand why the flush valve sits so high where the flapper is? What is the point of leaving that water in the tank?

Jeff86, Thank you for your interest in this model. You can adjust the water level on the fill valve which is located inside the tank. The fill valve will have a solid round top, then connected to, and extended out from the side of the fill valve will be a 3/8-in diameter hexagonal shaped water level adjustment rod sticking up with a hollowed out plus sign in the middle of it. To increase the water level, turn the rod clockwise to adjust the float cup. To decrease the water level, turn the rod counterclockwise to adjust the float cup. If that does not give you the results you are looking for, halfway down the fill valve, where the upper tube piece and the lower tube piece intersect there will be a plastic pin. Push down on the plastic pin to remove it. Then holding the lower tube stationary, gently twist the upper tube counterclockwise (approximate 1/8 of a turn) to disengage the upper from the lower fill valve tubes. You can then raise or lower the fill valve to adjust the water level. (Be careful not to raise the fill valve too high or the tank lid may not fit back into place.) Once the desired level is chosen, again hold the lower tube stationary and turn the upper fill valve tube clockwise (approximately 1/8 of a turn) to secure the selected level. Reinsert the plastic pin to lock the desired level into place.