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It seems to be a bug.

One thing that might work: While Edit Template in the template chooser does nothing, you can edit the template directly. Templates are in ~/Library/Application Support/The Omni Group/Omnigraffle/Templates. Double-click a template file there to edit it. (Just changing the default font there seems to do nothing, as you found with a new template.) Change the font and something else, say color, as the defaults for shapes in the template. Save it. Open the template again and set the color back to its original. Save it. The change in font may be retained when you do this, though it doesn't always work. (Make sure you're editing the template, by the way. If OG wasn't already open, opening the template to launch OG will also open a new-document window. Close that one to get to the template window.)