>Always flat:
>defaults write com.omnigroup.OmniGraffle PrivateGraffleFlatFile 0
>
>Flat unless there are images (the normal behavior):
>defaults write com.omnigroup.OmniGraffle PrivateGraffleFlatFile 1
>
>Always as a package:
>defaults write com.omnigroup.OmniGraffle PrivateGraffleFlatFile 2
(Use "OmniGraffle" or "OmniGrafflePro" as appropriate.)