Something to remember is that Perry was closer to being the straw that broke the Tokugawa camel's back, than the butterfly starting a hurricane.
By this point stuff would likely have happened largely similar, if prehaps a few other players in the tertiary gallery (prehaps as mentioned Putyatin replacing Perry, among others), and if beyond realistic chances Tokugawa manages to fend off the Satchou Alliance in the Boshin War, then another civil war would must likely had come again as soon as the least exhausted daimyo got his breath back. Exact differences between this hypothetical new winner and the Satsuma-Choshou Alliance are hard to guess at, but the overarching ambitions (make Japan sit with a strong hand, making equal treaties with the western world, instead of being maimed by unequal treaties such as China and the rest of Asia were) and their attempts to make it happen, would most likely similar in shape, if not in result (although there is no fundamental reason to believe that Satsuma and Choshou had any reason to be more likely to do it than others).