Joypad save autoconfig isn't working due to destination directory

The joypad autoconfig dir is set in the config file as:
joypad_autoconfig_dir = "/app/share/libretro/autoconfig"

If I manually assign buttons to a joypad and later decide to save this assignment as autoconfig, the saving fails as the application has no write rights to /app.

Saving personal autoconfigs is usefull when one has many joypads of the same type: it is only necessary to manually assign buttons once. This is specially important because using udev to access joypads isn't working, and basically all joypads need to be manually assigned.

I understand that the intention is to keep and update joypad configuration centrally through Flatpak, but:
1) There are exactly 6 joypad autoconfigs for SDL2, compared to about 200 for udev. So the provided autoconfigs aren't very useful.
2) Retroarch docs always suggest the user to use the online updater.
3) It seems reasonable to allow the user to save his/her autoconfigs.

If I set:
joypad_autoconfig_dir = "~/.var/app/org.libretro.RetroArch/config/retroarch/autoconfig"
and use the online updater, the app works as intended (minus udev)