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You can edit OmniOutliner's default template by going to the OmniOutliner preferences, clicking the General tab, and then the Edit New Document Template button. The problem is that you aren't creating a new document, you're opening an existing document, so new document templates don't come into play.

You might contact the Omni support folks directly (they aren't guaranteed to see or respond to forum posts) to make sure there isn't something I've missed that would solve this problem for you. Call them at 800-315-6664 or +1-206-523-4152 during Seattle business hours, or email omnioutliner@omnigroup.com.