I got the following certification error when submitting to the app store.
[My App Name] takes a dependency on Microsoft .Net Native Runtime Package 1.x framework but
I had the same error, and I found that ticking "Optimise Code" in build options made it go away.
I find that with Microsoft poke-and see is the most reliable technique.
Just had a similar issue. Try adding a PackageDependency line to the Package.appmanifest:
<Dependencies>
<TargetDeviceFamily Name="Windows.Universal" MinVersion="10.0.0.0" MaxVersionTested="10.0.0.0" />
<PackageDependency Name="Microsoft.NET.Native.Runtime.1.4" MinVersion="1.4.24201.0" Publisher="CN=Microsoft Corporation, O=Microsoft Corporation, L=Redmond, S=Washington, C=US" />
</Dependencies>
See: UWP App Package created with Visual Studio 2015 Update 3 won't install on phone