@mitu Thanks for responding. I figured out a solution minutes after posting my question... maybe.

My solution was (ironically) to "update all installed core packages" within RetroPie-Setup. This caused the missing "autoconfig-presets" directory to be re-generated in the correct place.

Everything seems to work fine for now, but hopefully doing this won't cause new bugs elsewhere. If I encounter any more problems I will also make sure
retroarch is updated.

To be a bit more clear: when selecting a non-working preset retroarch just dumps me back to the filter selection screen without making any changes.

Shaders can be set under retropie setup - Configedit (005), Configure basic libretto emulator options (0), configure default options for all libretto emulators