The victory of the pro-imperial Satchou alliance against the Tokugawa bakufu ultimately resulted in the Meiji Restoration of 1868, which set Japan on the path to rapid modernization. This involved the creation of a strong central government centered around the figure of the Emperor and the enforcement of universal conscription, which meant the abolition of feudal domains and ultimately of the samurai as a class (even though many in the new ruling class were former Satsuma or Choushuu samurai).
What were the reasons for some feudal domains to support (Satsuma, Choushuu, Tosa, Hiroshima, etc) and others to oppose (Aizu, Takamatsu, Sendai, Yonezawa, etc) the Meiji Restoration? Did the 1877 Seinan War show that many of the samurai who fiercely supported the Restoration didn't expect it to turn out the way it actually did? Did former clan rivalries survive the end of Japanese feudalism?
A lot of things to unpack here, as it is a very complicated point in Japanese history.
First, no one openly opposed the "restoration to direct rule" by the Emperor. That was already agreed upon by both sides in the autumn of 1867. In reality, both sides must have known that power and decision making would continue to reside with the leading domains. While other domains played important parts that resulted in this circumstance, Satsuma and Chōshū were really the only ones who pushed for war, as if things continued the way they were going, the Tokugawa would remain the leaders of the new government. This seem to actually have been preferable to the leaders of the other domains, but was unacceptible to Satsuma and Chōshū. You can read about that here.
The other domains (Tosa, Echizen, Hiroshima) only joined Satsuma and Chōshū's side when the emperor declared for Satsuma and Chōshū by allowing them to use a (newly-made) imperial flag in the middle of the Battle of Toba-Fushimi, which also caused many on the Tokugawa side (including branches of the Tokugawa family) to switch sides.
The northeast domains were not opposed to the "restoration to direct rule." Chōshū was out for Aizu's blood, and the northeast came together to beg for Aizu's forgiveness. Things went haywire and turned into open fighting for the northeast. See here.
After the war, abolishing the domains and samurai, rapid modernization, and universal conscription were pushed through by the leaders of the new government, who were front-line figures during the Bakumatsu. They were able to do this by quickly establishing the new goverment's army from a core of Satsuma troops. Having just experienced the Boshin War and the harsh punishment delt to the loosers, no one wanted to risk rebelling against the new government. Note that this move was done without explicit consent of the Satsuma daimyō, who gave Saigo Takamori an earful when he realized what happened but could do nothing to change the course the government was heading. And the terms of the abolishment of the domains were fairly generous to the old domain leadership, though not to the average samurai.
You can read about ex-samurai rebellions here. There definately were a lot of samurai who helped defeat the Tokugawa who were angry with the way the country was heading. However it's harder to say for the Seinan War. The leadership never expressed anything other than a feeling of injustice at the supposed attempt on Saigo's life, but we know the movement quickly absorbed disgruntled samurai from southwestern Japan, many of whom must have been angry with their treatment by the new government.
The Meiji oligarchy was predominately made of people from Satsuma and Chōshū. And while people from the defeated domains did participate in the new government, they were kept away from positions of power. There were definately regional ties to political grouping as well. For instance, Itagaki Taisuke's Liberal Party, which argued strongly against Satsuma and Chōshū's monopoly on power, had a good portion of the Tosa leadership. And Aizu for one still hasn't forgiven Satsuma and Chōshū.