Notifications don't appear the way they are set up in System Preferences

Are some third party apps not integrated into the OS Mountain Lion Notification Center even though they are listed in System Preferences > Notifications?

As an example, Viber notifications appear as a Banner type even though they are set to Alert type in System Preferences. In fact, I don't even think this Banner is generated by the Notification Center at all as the 'look' is different - I think it is generated by Viber itself. If I disable the notifications within the Viber app, but leave them enabled in System Preferences, no Banner/Alert appears at all...however a Badge icon does appear indicating a new message.