You can .NET Native on your own machine for testing but the package uploaded to the store contains MSIL. The final .NET Native version is then compiled in the cloud.
One great feature of .NET Native is that the compiler is capable of being hosted in the cloud. When you build your Store package in Visual Studio, two packages are created – one .appxupload and one “test” .appx for sideloading. The .appxupload contains the MSIL binaries as well as an explicit reference to the version of the .NET Native toolchain your app consumes (referenced in the AppxManifest.xml). This package then goes to the Store and is compiled using the exact same version of the .NET Native toolchain. Since the compiler is cloud hosted, it can be iterated to fix bugs without you having to recompile your app locally.
https://blogs.windows.com/buildingapps/2015/08/20/net-native...
One great feature of .NET Native is that the compiler is capable of being hosted in the cloud. When you build your Store package in Visual Studio, two packages are created – one .appxupload and one “test” .appx for sideloading. The .appxupload contains the MSIL binaries as well as an explicit reference to the version of the .NET Native toolchain your app consumes (referenced in the AppxManifest.xml). This package then goes to the Store and is compiled using the exact same version of the .NET Native toolchain. Since the compiler is cloud hosted, it can be iterated to fix bugs without you having to recompile your app locally.