Keep in context
It is important to remember that Know Your Enemy: Japan is a propaganda film and follows the same formula as seen in Nazis Strike and Divide and Conquer of Capra's Why We Fight series. Just as the Nazis are portrayed as the latest effort of German ambition to conquer the world going back to the 19th century so is the government of Tojo.
If anything Know Your Enemy goes 180 degrees from Prelude to War shifting the cause of the war from the Emperor to those around him. However the echoes of these earlier propaganda films runs through this picture making the film very schizoid. The first part (how the Japanese view themselves) has the Emperor wielding fantastic power while the second part (the external view) shows him as little more than a figurehead with those below him really calling the shots.
It is almost as if Capra and those over him did not know where to go with this picture.