How? Below sounds like maybe you edited a shortcut. That still works (but changed a bit).
Do you mean start at login? Any customized shortcuts will lose custom options on reinstall.
Bypassing Duplicati is always possible, e.g. type startup in Explorer then set up as you like.
I don’t know if any program changes can be done to guess correctly at what your goal was.
This is a bigger issue than before, because previously the autoupdate didn’t alter shortcuts.
New step is add --webservice-password=<password> in addition to --no-hosted-server.
Detached TrayIcon (a term I find to be a contradiction in terms) says how to attach TrayIcon.