Template are indeed a powerful feature, especially when used for personalization.
The disadvantage is that changing the platform-specific payload of a notification requires updating the registration.
Usually template registrations are a good fit for notifications that have always the same format and target multiple platforms
Using native notifications sending might enable you to easily target specific devices, however you can achieve the same goal by using Tags.
The bottom line is that I also see no real value in using the native notifications other than simplicity on the client side development.
I also wouldn't be surprised to find out that the Notifications Hub itself is using the templates to send the native notification (but that is of course an assumption of mine...)