(It didn't solve the weird sound error notification, but hey if it works it works!)
I think that sound/alsa error comes from EmulationStation, not fro the emulator. Use the EmulationStation menu and play with the Sound settings - Audio Card/Device are the ones that produce this error. Most likely you can change the Audio Card from Default to something else and the error will go away.
@DieKatz I just wanted to say thanks for noticing this problem. While playing Sonic 3 on my gpi I noticed that some of the sound effects weren't playing at all. I could never figure out what the problem was. It was the same stereo/mono issue as you were having. So thanks again!
So going back to HDMI I'd have to remove/comment audio_pwm_mode=0
You can quickly toggle the option from a script or the console by these commands:
# make a backup of config.txt
cp /boot/config.txt /boot/config.txt.backup
# switch to "1"
sed -i -e 's/audio_pwm_mode=0/audio_pwm_mode=1/g' /boot/config.txt
# switch to "0"
sed -i -e 's/audio_pwm_mode=1/audio_pwm_mode=0/g' /boot/config.txt
The lines beginning with # are comments and can be omitted. Mind the single quotation marks, they're important!
You could save them in convenient executable scripts in a (new) directory called "bin" in your home directory:
cd /home/pi # make sure we are at home
mkdir bin # create the directory "bin"
echo "sed -i -e 's/audio_pwm_mode=0/audio_pwm_mode=1/g' /boot/config.txt" > bin/pwm1 # write the first sed command to bin/pwm1
echo "sed -i -e 's/audio_pwm_mode=1/audio_pwm_mode=0/g' /boot/config.txt" > bin/pwm0 # write the second sed command to bin/pwm0
chmod u+x bin/pwm1 # make pwn1 executable
chmod u+x bin/pwm0 # make pwn0 executable
Since $HOME/bin is part of the console's search paths for commands and scripts, you can now just execute pwm1 or pwm0from any directory to toggle the option audio_pwm_mode between 1 an 0.
Besides that matter, do you know that you can enable an experimental audio driver with audio_pwm_mode=2? It fixed an annoying static noice on my Pi.
Can you try increasing the system's sound volume from a SSH or command line using alsamixer ? I know it sounds stupid, but maybe the default volume is too low for you to hear it.
Otherwise, you can enable verbose logging when starting a ROM with the Runcommand launch menu (https://retropie.org.uk/docs/Runcommand/#runcommand-launch-menu), play a bit, then exit and get the /dev/shm/runcommand.log file. Paste the contents of the file to pastebin.com so we can take a look at it.