The Pi Musicbox uses setsound.sh to set the volume level on every reboot. To ensure that the volume is set to your preference, you would change setsound.sh to include:
VOLUME=<your preference here>
…and then reference this value in:
# Set initial hardware volume
amixer set -c $CARD "$CTL" ${VOLUME}% unmute > /dev/null 2>&1 || true