The roles of the Sith Master remained the same throughout the war. Their powers did not. The powers given to the Sith Master varied, though most stayed the same. By the time Darth Nall, a law was introduced so he could have complete control over all groups affiliated with the Separatists, to much outcry. Luckily a civil war between them did not erupt due to nearly all of the fortress worlds being captured by the Republic.