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Sorry, neither of these behaviors are currently possible in OmniGraffle.

We've existing requests for both of these in our database; I've added your comments to them.

Depending on your situation, you can apply automatic layout to a selection of objects by using Arrange → Diagram Layout → Lay Out Selection. So creating your chart with Auto Layout off, then selecting only objects that are of lower rank might help.

If anyone else is interested in seeing this, feel free to write in to and we can add your comments to the feature requests!