By Revenge of the Sith, the fate of the Trade Federation is described as:
With Nute Gunray's death in 19 BBY at the hands of former Jedi Anakin Skywalker, now Darth Vader, the Trade Federation fell. Acting Viceroy Sentepeth Findos who was on Cato Neimoidia resisted for a brief moment but was forced by Stormtroopers to sign a peace treaty with the Empire only a few days after the Clone Wars ended, giving all of the Federation's resources to Palpatine's disposal to help him build the Galactic Empire but there was still some resistance. This had made the federation a puppet government of the Imperial Senate.
Emphasis mine. But the federation is described as:
The Trade Federation was a very powerful Republic commerce guild, trade cartel, megacorporation, and lobbying group that was founded in 350 BBY as an association of business and trade groups with its own commercial trade fleet.
The Federation grew to dominate entire star systems and all major trade routes, and possessed a formidable private military.
Which seems to make it many things, but not really a government. Yes they rule. They even have viceroys, so they clearly have local administrations setup. It just seems unlikely that a megacorporation would be so tied so a single ruler that one viceroy could lead to the dismantling of the whole thing by signing a piece of paper. It would be like assuming Steve Jobs could hand Apple over to the state of California with just his John Hancock. It might behave like a government in many ways, but it is a private institution with what sounds like a large number of stakeholders.
Do the novels or any other in-canon references provide greater detail to this? Some unmentioned manipulation by Palpatine perhaps?