If my reading is correct it seems that the .Net Native compilation is automagically enabled MSDN - Getting Started with .NET Native . I see that it may apply to newly created Windows Store Apps but I am also curious to previously created Store Apps that were created in my Windows 8.1 prior to upgrading to Windows 10. It's confusing because Visual Studio 2013 allowed you to enable this feature and I currently do not see it even after creating a new application.
Unni discussed the use of .Net Native in his build session Deep Dive into XAML and .NET Universal Windows App Development
From slide 9:
All Universal Windows 10 .Net apps delivered to consumer devices will be compiled with .Net Native
Windows 8.1 apps aren't automatically delivered as .Net native.
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