It's not actually surprising that Japan is like OTL in Runa's timeline. It's not exactly a Korea-like situation. North Japan was only Sakhalin, not a 50% split.
So in OTL, after the VE-Day (8 May, 1945) USSR voided it's non-aggression treaty with Japan (8 August), invaded South Sakhalin (Karafuto) and the Kurils (Chishima). Today only the sovereignty over the four southernmost islands is disputed (although de facto they are a possession of Russia).
Seeing how in Runa-verse the Kurils are still Japanese, the most likely explanation is that the Soviets moved to secure Sakhalin in light of a Japanese surrender (Sakhalin was split in half after the 1904-1905 Russo-Japanese War, which made a land invasion possible). But unlike OTL, they couldn't take the Kurils (in OTL Soviet Invasion was made possible thanks to American naval vessels). I'm guessing that a conditional surrender meant, that USSR could not annex the territories as part of a peace treaty, so they set up a puppet government to justify the occupation.