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There is something wrong with the newest Preferences -- it doesn't offer anything else but to edit the startup template (which opens automatically whenever you start the program).

However, the Help still refers to choices (the first 2 are missing):
When OmniOutliner starts up

- Select the Open documents which were open last time you quit to keep a consistent workspace between OmniOutliner sessions.
- The Create new document checkbox gives you a new, untitled document to work on each time you start OmniOutliner.
- The Edit New Document Template button opens the default new document template outline; any changes you save to this outline will appear in each new outline you create.
That's OO Pro v.3.10.2.