Reversing the second cell does not prevent it from getting contact in most flashlight designs. When both cells are from the same lot the electrical potential between the ends of the batteries is zero (you can verify that by putting two batteries together in the configuration they'd have in the flashlights and meassure the voltage between the free contacts). Thus there will be neither accidential drain nor shorting will occur when you leave the switch on.
This method would only be useful for flashlights with two cells. In other types the reversing of one cells may result in reversing the current in that cell which is even worse than just shorting it. So the habit of locking the switch or putting a small plastic disk on top of the last cell is safer.