.NET Native was experimental in WP 8.1 and W8. On 10, it becomes mandatory and you couldn't even publish a JIT .NET app to Store.
WP 8.0 didn't even had WinRT, only Silverlight apps, and all JIT. If you wanted native in 8.0, had to go with C++.
About Desktop, C++ was rarely used. Most apps were either .NET C# (JIT) or WinJS. JIT WinRT .NET was super slow, WinJS apps were even faster, which is why many apps were all WinJS, including inbox Windows apps, like the MSN apps.
Some people really have very selective reading capabilities.
"When you build your app in Visual Studio, the code is not compiled into a native image, but into a machine-independent Common Intermediate Language (CIL) binary file. (CIL was formerly known as Microsoft Intermediate Language, or MSIL.) This CIL file is what you submit to the Store when you’re ready to sell your app. At that time, the binary file is converted from CIL to optimized Machine Dependent Intermediate Language, or MDIL. Finally, when the user downloads your app to a device, the MDIL file is linked to produce a native image. These steps are repeated in your development environment whenever you deploy your app to a Windows Phone 8 device.
Pity that the Channel 9 videos on MDIL for Windows Phone 8 are no longer around.
WP 8.0 didn't even had WinRT, only Silverlight apps, and all JIT. If you wanted native in 8.0, had to go with C++.
About Desktop, C++ was rarely used. Most apps were either .NET C# (JIT) or WinJS. JIT WinRT .NET was super slow, WinJS apps were even faster, which is why many apps were all WinJS, including inbox Windows apps, like the MSN apps.