To clear any configuration changes, first make sure that cloud saves are turned off. The game will sync your original preferences before launching. This was the only way I could delete any configuration so that I could stop the game from launching in windowed mode, which only showed a black screen.

To reset your configuration settings:

Disable cloud syncing.

Delete all files under:

./.steam/debian-installation/userdata/96909919/388410/remote/ and ./.steam/debian-installation/steamapps/compatdata/388410/pfx/drive_c/users/steamuser/AppData/Local/Darksiders2/

Launch the game, make your changes.

Re-enable your cloud syncing.