Can't save settings changes on Steam Deck

Description

Any changes I make to RetroArch's settings are not being saved on exit. I don't see any messages that appear to explain this in the
log output, or any changes to ~/.var/app/org.libretro.RetroArch/config/retroarch/retroarch.cfg or any other files in that directory. I wasn't able to get support for this issue on the Discord and it appears to be a bug.

Expected behavior

RetroArch settings are saved on exit.

Actual behavior

My settings changes are not saved on exit.

Steps to reproduce the bug

1. Run RetroArch, either on the command line or from the main menu in gaming mode.
2. Change a setting, e.g. one of the hotkey assignments or the sound driver.
3. Exit the RetroArch GUI.
4. Reopen RetroArch, observe that my changes have been reverted.

Bisect Results

It also occurs on 1.12.0, the oldest version I could downgrade to via Flatpak.

Version/Commit

• RetroArch: 1.16.0

Environment information

SteamOS Holo, version 3.5.7, build 20231122.1

Start by reproducing the issue on SteamOS Holo through the command line or Gaming Mode, then inspect the linked retroarch.log and ~/.var/app/org.libretro.RetroArch/config/retroarch/retroarch.cfg after changing a setting and exiting. Compare whether the configuration is written or restored on relaunch; done means settings changes persist across exit and reopen.