The [Skyrim|Enderal].INI file is used to read the list of vanilla BSA files to load.
The Fatal: Could not find ini error message signifies that the INI file can not be found or access is denied.
Starting the game launcher once creates the default INI files. The game launcher can be started directly from a file manager like Windows Explorer without Steam to avoid game updates. Exit the launcher instead of starting the game.
If the shown game mode is wrong, start the tools in the desired game mode.
In case existing files can not be accessed, add an exception to whatever it is that is blocking access.
Alternatively set the path to the INI with a command line argument. If the path to the INI is already set with command line arguments, make sure they have been added correctly.