Well, no sooner do I ask this question than I come across a solution that works.
By settings the EmulationStation volume to 75% (so snaps play well)
Modify /opt/retropie/configs/all/runcommand-onstart.sh to have the line amixer set PCM 40%
Modify /opt/retropie/configs/all/runcommand-onend.sh to have the line amixer set PCM 75%
Ideally wouldn't need to do ...