The problem with this idea is that if by some unfortunate accident of history, Nazis gain power again, they'll say exactly what you just said except replace the word Nazi with Jew.

I would flip what you just said on its head and say practically the opposite: the virtue of Mastodon is that when the Nazis seize power not all instances will be forced to censor Jews (whereas Twitter will be forced to do it or shut down).

What exactly is your threat model — every single country will simultaneously become a nazi dictatorship? Is their a world domination beforehand which somehow misses the “nuke the Earth” part?

For a server to operate you only need a very basic power source and internet connection, even in an occupied country it seems plenty doable.

Example: an extremist government comes into power in the US and orders all social media and traditional media companies to censor a certain type of speech. They could very well have popular support if there has been a war or a depression or some other crisis, it was only 75 years ago that we had a literal Office of Censorship, were putting Japanese-Americans in internment camps etc. US media is very concentrated today, the government only needs to go around to a handful of companies to censor the vast majority of outlets Americans get their news from.

Sure someone can set up a server somewhere and publish whatever they want but if no one reads it it won't really matter. Most people won't change where they get their news overnight even if the government does impose censorship. That's why federated social media is so valuable, widespread use of it ASAP is a benefit to society. It can de-concentrate the ownership of media distribution, decentralize control and make the next Office of Censorship's job much harder.