After I update the SteamOS 3.5.5 , I want to update/install the flatpak packages with flatpak update -y. this command does not worked and I need sudo access for that. Is this become rule of thumb for flatpak packages for this update?
Flatpak without --user changes flatpaks system wide, irrespective with which user it's run. By using --user flatpak's are stored in the home directory (.local, I believe).
Most distros ship with system wide flatpak remotes, so --user isn't necessary.