There's no extra commands in EmulationStation or otherwise that changes the resolution on a stock RetroPie installation. You can change the emulator resolution via from the runcommand launch, but that's about it.

If 240p set via config.txt works, then I don't see why the same method for 480i wouldn't work. How are you setting the 480i resolution for your display - via config.txt or other method ?

Please also add the info asked in https://retropie.org.uk/forum/topic/3/read-this-first to your post (RetroPie version, devices, etc.)