The filesystem is locked as read only, this is for good reasons so strongly reccomended to find ways to keep it and just add extensions rather then set the filesystem to rw and for the gameplay experience to be impacted.
I followed this: https://blogs.igalia.com/berto/tag/steam-deck/ ...to make the extension and get it registered, then used this: https://www.reddit.com/r/SteamDeck/comments/vocyi5/start_syncthing_automatically_on_steamdeck_even/ tp setup the systemd services and get them running on startup
Still not clear how I can do this for vscode for example. It seems like the main idea is to use flatpak (I did that for barrier, and that's working nicely).