The Instrument of Surrender contains the provision that "The authority of the Emperor and the Japanese Government to rule the state shall be subject to the Supreme Commander for the Allied Powers who will take such steps as he deems proper to effectuate these terms of surrender." (The first of these terms being the acceptance of the Potsdam Declaration and its provisions.)
I'd be interested in your opinion as to what else would have been accomplished had the instrument contained an explicit surrender by the Government. You state that it is an important distinction, and I'd like to get your thoughts on what was so important.
Certainly. While the instrument of surrender does make the Japanese civilian government subordinate to MacArthur's Occupation forces, it did not require the surrender of civil authority to Allied command, as was the case in Germany.
The reason for this was because unlike Nazi Germany, the Japanese government not only fufilled constitutional, civil needs, but reflected cultural norms as well. The Japanese public could accept the surrender of it's armies to enemies that had clearly demonstrated their superiority in the field (this is a near-universal oriental concept, see Sun Tzu, Confucious, et. al.). However, civil authority in Japan devolves from divine providence (i.e. the Emperor) and therefore, turning over civil authority to the Allies is, in a sense, religiously intolerable.
What occurred during the American Occupation of Japan is that MacArthur, fully aware of these distinctions and cultural bugaboos, left the visible signs of Japanese self-rule in place, and worked behind the scenes through the Emperor to affect whatever changes he deemed necessary (New constitution, reorganization of the civil service, universal sufferage, etc). MacArthur could dictate to the Emperor and the Emperor to the government and people. To do it any other way would have incited the Japanese to continue the war.
That is the distinction; Germany could function without the Nazis, Japan could not without the Emperor and the organs of government that were touched by his divine mantle. There was no strict program of "De-Nazification" in Japan (with regards to the militarists who dragged the country into war), because to do so would have resulted in civil unrest on a huge scale (and would probably have driven Japan in to the Communist sphere). For the sake of peace, the Allies were willing to make these concessions to the Japanese people.