yes, it should, there is code specifically checking if the path to the game is epic games, steam, or anything else. though, if you have WoG2 on other platforms, they might be worth a try because i relied on community feedback for epic games compatibility
are you sure there is nothing located at %APPDATA%\Godot\app_userdata\Level Juicer? this is assuming youre on windows, im not sure what the filepath is on other operating systems.