If you set CI3's 'composer_autoload' config value to TRUE, it will look for /application/vendor/autoload.php. However, you can choose to set it to a string containing the path to your autoloader, so your directory structure would work as well if you set the value to either the absolute path or '../vendor/autoload.php'.
Of course, if you're using another method to load the Composer autoloader, it won't really matter.
The /application/third_party/ directory is often used by developers who wish to distribute their code/packages for use by other developers. Then the code supplied by those developers is in a location somewhat isolated from your application.
