They can block Signal because it is centralized. Signal knows this and built proxies into the app for this purpose.

Similarly they can block the main matrix.org server but since it's decentralized you can still use any of the thousands of servers they may not even know exists.

Russia's long term plan seems to be blocking Western networks and force the bulk of domestic users to the Max messenger, which implements inspectability a la ChatControl. Apropos: https://fightchatcontrol.eu/

You can tunnel through the Great Chinese Firewall fine, if you know what you're doing.

I don't know what you mean, e.g. GrapheneOS and AOSP based ROMs are all open source. Linux (or *BSD) on mobile devices is also an option.