It is by design. The GUI needs to read the settings file from a known location to know where else to look for the blockchain if you change it. I could have opted to store the path to the config file, or all the config options themselves within electron's localstorage -- but in my opinion that just adds unnecessary complexity. In the case that there are any issues with the config file, it is easier and more user friendly to have the settings file in a default location that the user can either edit with notepad, or just delete (forcing the wallet to go back to the welcome screen.)