If I create a project using the Cordova CLI, add a plugin such as https://github.com/litehelpers/Cordova-sqlite-storage (which installs a C++ component for the Windows (Universal) target), add the windows version, and try to run the project with the default selection of All CPUs (or Mixed Platforms on Windows Phone), VS complains that SQLite3.winmd is not found. But if I select a particular CPU such as x86 or x64 and try to run, then it will build the SQLite C++ library, build my project, and run.
The workaround is to omit SQLite3.Windows.vcxproj & SQLite3.WindowsPhone.vcxproj from plugin.xml, and install them manually. I tried to describe this workaround in the readme.
The recommended solution is to add support for "Mixed Platforms" and "Win32" to template/CordovaApp.sln in the cordova-windows project.