The difference is the number of points you would get from each purchase. Every purchase in the Webstore VIP Program gives VIP Points, but that's not the case for purchasing in-game from the Premium Store!

The number of points may differ between the two platforms. The same bundle on the VIP Program website will give more VIP Points than the in-app Premium Store.

There are also bundles exclusively available in the VIP Program, so be sure to log in and check them out!