Quickly scanning material on the Graphviz engine which OmniGraffle is using, I get the impression that simple trees with parents centred over their children really are beyond the scope of that engine :-)

I hope that this is a misapprehension ...

( but if a clean and compact orthogonal layout can be hacked with a simple applescript by a non-programmer, then I am sure it is not beyond the enormous wisdom of OmniGroup's esteemed collectivity of creative engineers and brilliant wizards :-)

Worth requesting a "Centre parents over children" option for Automatic Layout through OG Help > Send Feedback, I think ...

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