Fascinating... simply fascinating.
Turn off "Compile with .NET Native tool chain" on the Build properties of the main UWP app. UWP libraries don't appear to offer the native tool chain option.
I was fighting the issue of why my file parsing application took about twice as long to execute (not build) as a release build than as a debug build. Completely the reverse of what should have happened. I also happened to note the long time to complete the release build, but it was a secondary issue for the time being.
If you watch the output window during a complete rebuild, you'll note any libraries you have will build as quick as you're used to. Then the main app will be the one that bogs down -- a LOT.
Check the Build properties for your projects and note only the main UWP app has the "Compile with .NET Native tool chain" option. The libraries don't have it. Also, by default only the release build has it enabled. The debug build doesn't. Sure enough, turn it off on the release build and the release build starts completing as fast as the debug build.
Then strangeness of strangeness... my UWP app release build now runs about 10% faster than the debug version when it used to run nearly twice as slow.
This is all VERY counter-intuitive. A native build should run just as fast, if not even a tiny bit faster, than the non-native build. The compiler under Visual Studio certainly has the option of putting much more hard work into optimizing the build for the processor.
I wonder if there is anything else published about problems with the native build tools, and whether there's an explanation. The slow build time I can understand completely if the build tools are munching away a lot harder trying to optimized for the specific native processor. However the fact the native code runs dramatically slower than the non-native code is completely counter-intuitive. It doesn't seem to make sense that MSFT would have bothered to release the native build tools under such circumstances, which leads one to wonder if the tools are being used incorrectly or some other misunderstanding is a'foot.