Are you looking in the right place for the config file?
I haven't had a chance to download and install this game yet, but with the Linux versions of other Beamdog games, the config files are found in these locations, respectively:
BG2:EE, patch 1.3: ~/Documents/Baldur's Gate II - Enhanced Edition/Baldur.ini
BG2:EE, patch 2.x: ~/.local/share/Baldur's Gate II - Enhanced Edition/Baldur.lua
IWD:EE, patch 1.4: ~/.local/share/Icewind Dale - Enhanced Edition/Baldur.ini
...i.e. not in the game installation directory itself. And note that the 2.x patch switched from an .ini file to a .lua file. Also, you have to start and close the game at least once for the file to be created.
Post edited April 12, 2017 by archy2