Silent installs or how to create the necessary msi files

Are you sure you need that? Could you test some msiexec options such as /quiet?
Unattended silent installation in Windows used a different option. There are a bunch.

You want to hardcode that in the .msi (not that I know how)? How about job import?
Duplicati.CommandLine.ConfigurationImporter.exe should be able to do that.