Auto Update Settings: Docker, Update Check Frequency: Disabled, Then either either update all applications, or set it to no and cherry pick what you want updated.
Backup Settings: Update Applications on Restart: Yes
Edit: Even though it does come with basically that as defaults, because the cfg file doesn't exist, Backup assumes you don't want it to run. Make a change, any change in the settings, change it back and apply. The cfg file will get written.