@Vealmike I may be a little late to the party, but had a similar need this week. Following @Clyde 's suggestion, I tried bind mounting the USB stick via /etc/fstab, but the timings were off and the bind mount was done before the USB stick was actually available.
What I ended up doing, and is working is actually hook into the autostart.sh script. Essentially adding this:
# Wait at most 1 minute for the USB drive to be mounted
# And link the config folder
ATTEMPTS=6
USB_DRIVE='/media/usb0'
i=0
until [ "$i" -ge "$ATTEMPTS" ]; do
grep -q -s "$USB_DRIVE" /proc/mounts && \
sudo mount --bind /media/usb0/retropie-mount/configs /opt/retropie/configs && \
break
i=$((i+1))
wait 10
done
at the beginning of the script. It has some basic logic just to attempt 6 times with 10 seconds delay between each until the stick is detected to be mounted, and then proceeds to do the bind mount of the configs folder, before actually starting emulationstation (or whatever is defined to auto start).
I know it's been three years since your post, but maybe this will help someone (like me) in the future 😁
