You can install Duplicati as a service. Regular user normally cannot start or stop system processes.
As a plus, Duplicati won’t be executed twice if both users are logged on to the same machine.
One caveat is that Home directory has to be included by absolute path (C:\Users[user]) instead of environment variables (%USER% / %APPDATA%)
References:
Disable autostartup on initial installation
Install Duplicati as a service
Use portable mode to prevent configuration loss on next Windows Update