How to reproduce:
1. Create a new empty project
2. Switch Target platform to UWP
3. Set 'Scripting Backend' to IL2CPP
4. Build the project
5. Open the PowerShell in the Build directory
6. Execute the following commands:
1. $msbuild='C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\MSBuild\15.0\Bin\MSBuild.exe'
2. & $msbuild .\<PROJECT-NAME>.sln /t:"restore,build" /p:"AppxBundle=Always;AppxBundlePlatforms=x86|ARM" /p:Configuration=Master > build.txt 2>&1
3. $LASTEXITCODE

Expected result: "0" is printed out (meaning that the building was successful)
Actual result: "1" is printed out (meaning that the building failed)

Reproducible with - 2017.4.0f1, 2017.4.29f1, 2018.4.3f1, 2019.1.8f1, 2019.2.0b8, 2019.3.0a8

UPDATE:

This is caused by a "feature" in MSBuild were the output directory is nested when performing a multi-platform build. This functionality must be explicitly disabled to build the Unity generated project. The issue is discussed on these MS developer sites:

https://developercommunity.visualstudio.com/content/problem/164983/creating-uwp-appxbundle-works-in-vs-store-wizard-b.html
https://github.com/microsoft/MixedRealityToolkit-Unity/issues/7351
https://github.com/Microsoft/msbuild/issues/2445

To work around this issue pass: "/p:UseSubFolderForOutputDirDuringMultiPlatformBuild=false" on the MSBuild command line.
For example:

& $msbuild .\<PROJECT-NAME>.sln /t:"restore,build" /p:"AppxBundle=Always;AppxBundlePlatforms=x86|ARM" /p:Configuration=Master /p:UseSubFolderForOutputDirDuringMultiPlatformBuild=false > build.txt 2>&1