If re-packaging an app with multiple shortcuts, one of them becomes the default entrypoint to launch when the package is installed on end-user machines. It isn't clear how that is selected, but it does look like the top one in the manifest is it.
While you can manually edit the manifest, we should prefer packagers not do that when possible. Therefore a good solution to setting the default launch would be to provide a selection dialog in the "First launch tasks" dialog of the packaging tool. Up/Down arrows would suffice.