It should be possible. The newest RetroPie-Setup script has an updated runcommand.sh. https://github.com/retropie/RetroPie-Setup/blob/master/supplementary/runcommand.sh
runcommand.sh 7 => composite PAL
runcommand.sh 8 => composite NTSC
It would be nice if someone could test these new options.
It is now also possible to set audio output from emulationstation (update-> source-based-installation/emulationstation).