Thank you Mitu, but for me, a power-user at best, thats going to be like looking for the proverbial needle. Before I spend hours trying to troubleshoot this Ill just save my roms and do a fresh install.
#uncomment if you get no picture on HDMI for a default "safe" mode
#uncomment this if your display has a black border of unused pixels visible
#and your display can output without overscan
#uncomment the following to adjust overscan. Use positive numbers if console
#goes off screen, and negative if there is too much border
#uncomment to force a console size. By default it will be display's size minus
#uncomment if hdmi display is not detected and composite is being output
#uncomment to force a specific HDMI mode (this will force VGA)
#uncomment to increase signal to HDMI, if you have interference, blanking, or
#uncomment for composite PAL
#uncomment to overclock the arm. 700 MHz is the default.
#Uncomment some or all of these to enable the optional hardware interfaces
#Uncomment this to enable infrared communication.
#Additional overlays and parameters are documented /boot/overlays/README
Using raspi-config to change the audio output will not write to /boot/config.txt, but will change the ALSA (sound system) settings.
Changing the settings from the raspi-config will invoke
amixer cset numid=3 2
underneath. Try running this command from the command line (exit EmulationStation via the menu or by pressing F4) and see if the settings are kept after a reboot.
If that doesn't work, then add more info about your system, as detailed in https://retropie.org.uk/forum/topic/3/read-this-first.
So apparently I'm an idiot. Following the guide over at Reddit, I missed one thing. I had the mini-hdmi cable plugged into the second port and not to the port closest to the power supply. Looks like everything is working now.