The fundamental difference is that with Mastodon, or any Fediverse service, the server still has full control over the user. It's basically no different from regular Facebook or Twitter, just with some optional federation on top that can be switched off at any time (and often is).

On Nostr the server is just a dumb relay, it controls and owns nothing. User identities are proper public key pairs. If a relay goes evil, you can just use another one or use multiple at once to begin with, since the location of the messages is irrelevant, everything is held together by public keys.