I guess I’m not really sure why you are making this so complicated. Why not let Duplicati.GUI.TrayIcon.exe run for each user that logs in. (This is how the installer sets things up by default, by adding that shortcut to the startup folder.) The TrayIcon process will automatically choose an available port. No need to manually assign port numbers.
Edit: That’s right, you don’t want some users to get notifications. So for those users you could put Duplicati.Server.exe in their startup. But my main question is - why hard code any ports at all? Let the ports get assigned automatically.