Dolphin on emuelec 4.5, does not load the GameSetting ini file when loading the game, therefore it doesn’t override the Dolphin.ini base configuration for the game specifically. Not sure if on 4.4 version this issue also happens.
Example: For game Eternal Darkness we need to set GPUDeterminismMode to ‘fake completion’. This is already defined on the GED.ini file, that relates to Eternal Darkness game specific settings. But it won’t load when the game starts.