The packaging tool fails in the example of the subject.
I am aware that AppX shortcuts don't have arguments, but there are many MSI apps that use them and we need support for them in MSIX.
It appears that the manifest schema for the Application element does not have an arguments parameter, and that when creating the package, the tool finds the first shortcut and creates the Application element, and then for subsequent shortcuts skips them because the element is already present.
Either the schema needs extensions, or the tool should automatically detect the presence of arguments and remediate (possibly using launcher programs, but I hope not).
This issue is related to the previously reported issue
regarding lack of command line arguments, but reported separately because additional work will be needed on the tool once the first issue is solved.