Below is an example spotify-flags.conf file that defines the flags --disable-gpu-shader-disk-cache:
~/.var/app/com.spotify.Client/config/spotify-flags.conf
# This line will be ignored.
--disable-gpu-shader-disk-cache
This package enables the flags to run on Wayland, however it is opt-in. To opt-in run:
flatpak override --user --socket=wayland com.spotify.Client
To opt-out:
flatpak override --user --nosocket=wayland com.spotify.Client