The "Per App VPN" is a way of making sure apps on an iPhone that do not have encryption can be directed to go through a VPN process over the network so that information is not passed in the clear. This is very important to the enterprise level for security. If a FileMaker Go client connects to a FileMaker Server where the Admin Console has turned on encryption, then this is already taken care of. Basically, there is about 10-15% speed reduction for the encryption, but most all of my clients think that is worth the security.
Since the Per App VPN is a new feature in iOS7, I suspect this and other iOS7 things (e.g., maybe finger print ID) maybe be apart of FileMaker 13's future. Who knows. But I sure hope so!