sure! didn't want to imply that, it just was a major roadblock for me yesterday and today and a lot of searching around just showed that a bunch of people had the same problem. the solutions with manually editing the config file sure help but it would have been just so much easier if I could have set it in the menue. not because editing the file is difficult, more like you don't think of it because everything else just works like it should (well, beside the playstation classic controller not working despite being a simple USB device) and the config tool just blanking out is confusing. honestly if the whole system wouldn't crawl around at around 10 - 15fps at 4k you wouldn't even notice the problem is there to begin with. I'll search if the problem is known at Raspbian.
I don't think it would be 81, but you are correct that it's wrong. Shouldn't be 16 because my TV only displays up to 720p, not 1080p. Although it is a 16:9 TV (not 64:27 like it shows under #81). Also, my TV frequency isn't 30Hz, unless I'm missing something.
you've fixed it now so i guess this is irrelevant but yes, you'd need to use hdmi_group=2 for 81 - it doesn't seem to be supported under 1. but yes, @mitu 's suggestion would get show you the complete list of supported modes. given that it's less than 4k, i would always want to be running in the native panel resolution so you don't get scaling artefacts.
i assume now you've taken out hdmi_safe you can safely take out any hard coded modes and it should hopefully choose 1366x768 by default.
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.