Win8 appstore is for Metro apps only
the follow me everywhere app settings
Don't know about that - but you should probably be able to fudge your own there. It might be exposed over COM (since the usermode WinRT classes are built on top of COM).
and especially the siloed features that provides the user with assurance that the app will not hijack their PC in a virus like way.
That's a kernel protection mechanism and will be available to all user-mode processes, although I'm not sure if they've announced how you're supposed to do it. This is used by IE10 for instance to "sandbox" the page rendering process.