As I looked into the case description and checked the group policy "Automatically check for software updates" is actually deprecated and will be removed in future releases of DirectControl for Mac.

Therefore, as a workaround for modifying the auto update settings, please see the following method in order to modify the settings at App store via GP and command:

1. Go to the GPO at: Computer Configuration > Policies > Centrify Settings > Common UNIX Settings > Specify commands to run
2. Add the commands for the desired settings to enable. No need to add sudo.

- Automatically check for updates
defaults write /Library/Preferences/com.apple.SoftwareUpdate AutomaticCheckEnabled -bool TRUE

- Download newly available updates in the background
defaults write /Library/Preferences/com.apple.SoftwareUpdate AutomaticDownload -bool TRUE

- Install app updates
defaults write /Library/Preferences/com.apple.commerce AutoUpdate -bool TRUE

- Install OS X updates
defaults write /Library/Preferences/com.apple.commerce AutoUpdateRestartRequired -bool TRUE

- Install system data files and security updates
defaults write /Library/Preferences/com.apple.SoftwareUpdate ConfigDataInstall -bool TRUE
defaults write /Library/Preferences/com.apple.SoftwareUpdate CriticalUpdateInstall -bool TRUE