Pending surrender, the Japanese government would be overwhelmed by millions of refugees and unable to move food and other critical supplies to meet civilian needs. Regarding surrender, factions within the Japanese military were determined to fight to the death.
Historically, Hirohito decided to surrender and the cabinet and military command carried it out. They defeated abortive coup attempts to prevent or refuse the surrender. But the Japanese government was still essentially in place and the military leadership was not disrupted when this happened.
Operation Downfall would have disrupted the Japanese chain of command. Tokyo occupied. The Emperor and the cabinet in hiding, perhaps even prisoners of the Americans. Different regions and surviving Japanese military formations isolated from one another and under American attack.
In that chaotic situation, would the Japanese government even *be able* to surrender in an orderly way? Or would it just all fall apart, with some units surrendering with or without orders and others deciding to fight on hopelessly? How many people would die while that process worked out?
A best case scenario would probably be something like Hirohito realizing at some point that the war was lost and ordering a surrender while he still had the command and control to do so. A worst case scenario is apocalyptic.