No, WP.pro does not modify the default WordPress setup during installation. WP.pro adheres to a principle of delivering WordPress exactly as it is provided by WordPress.org. This means:
Default Settings
WP.pro uses the default WordPress settings.No Pre-installed Plugins
WP.pro does not install any additional plugins.No Removal of Plugins
WP.pro does not remove any plugins that come with WordPress by default.Unmodified Core Code
WP.pro does not alter the core WordPress code.
However, WP.pro does set up WordPress for you, which includes modifying the wp-config.php file as necessary for your environment.