The configuration file is overwritten each time the game is started, I assume because the game naturally modifies it in a way that makes it incompatible with Wine? Or at least some settings must not be modified.
The file is overwritten with the version that can be found at the root of the virtual drive (~/.PlayOnLinux/wineprefix/WorldOfWarcraft/drive_c/Config.wtf), so that's the one you want to edit to change settings permanently.
What I suggest is:
- start the game
- make the settings modifications you want
- exit the game
- open both the configuration file above and the one in the game's directory
- backport the settings you're interested in, don't change anything else
Hopefully not backporting anything incompatible.
Unless that whole mechanism is no longer necessary? I didn't wrote this script and don't own the game, so I can't tell...