On the wikipedia page Occupation of Japan it says: "Unlike in the occupation of Germany, the Soviet Union was allowed little to no influence over Japan." But gives no references or explanation.
I tried searching online for anything relating to this and I only managed to find 1 article on the subject. Read it here.
It basically says it might be because the Soviets were intimidated by the atomic bombs, but then "disproves" that by giving counter examples of other areas at the time where they refused to be intimidated into making concessions even under explicit threat of being nuked.
It then says: "Attractive for geopolitical reasons, Hokkaido was not part of the deal agreed upon at Yalta in February 1945. Stalin knew that by violating this agreement, he risked undermining Soviet gains in the Far East, including possession of southern Sakhalin and the Kuril Islands."
This makes a lot of sense, but then it says further on that Stalin changed his mind on the matter later on. Maybe it was too late by that point? I don't know.
I am very interested in this topic. Does anyone have any links or insight that they could share? I would appreciate it.
More can always be said on this, so anyone with insight should feel free to chime in! For the meantime, OP, you may be interested in u/kieslowskifan's examination of just this matter.