By default we don't use site settings we use user.config settings for smtp.
The only reason yours is using smtp settings from site settings is becuase you set this to true:
<add key="EnableSiteSettingsSmtpSettings" value="true" />
With that set to the default of false smtp settings are used from user.config
The only real advantage of using smtp from site settings is if you have a multi site installation and need to use different smtp settings per site or you just prefer to set those from the UI instead of from user.config.
See also Email Configuration
Hope that helps,
Joe