Removing the "Microsoft.Windows.SDK.BuildTools" package that comes with the Packaging Project solves the problem. This package is not mandatory.
The Windows Application Packaging Projet is required for example when including Win32 exe into an UWP project (runFullTrust capability) for publishing on the Store, otherwise the Store application can fail to start ( Store version of UWP Package with a full trust process forms app keeps crashing on launch )
In the detail, as mentionned by Hugo the AppxManifest.xml from the .msixupload file contains two "Makepri.exe" in the "build:Metadata" section: one "MakePri.exe" (capital "M") and one "makePri.exe" (lower case "m"). The "Microsoft.Windows.SDK.BuildTools" package is responsible for the "makePri.exe", when checking its "Microsoft.Windows.SDK.BuildTools.props" file.
Removing the package doesn't result in errors when generating the Store package or using the application.