How about adding a “Disabled by default” checkbox in the “Properties” panel of a game object? If this checkbox is checked, the game object will be disabled once it gets ready (or simply not enable at the beginning). Also the content of this game object won’t be shown in the editor’s preview (like what the action “Hide Objects” does).
Then, there is no need to write code to disable everything when initializing (e.g. in the function
init() in a manager’s script). That would provide some convenience, especially in the case of making menus and scenes.