[forum member]

As far as I am able to tell, OmniOutliner draws templates from
1. <your computer>/Library/App Support/OO3/Templates
2. <your home folder>/Library/App Support/OO3/Templates
3. built-in templates within the application itself

I'm having a little trouble following your description, so I'm unsure if this is going to be of any assistance.

I was having similar issues when working with templates. And it seemed like the more I fixed it, the more screwed up it became. And I couldn't figure out why. What I finally did was move all the templates from everywhere on my hard drive into one folder. I then moved all those templates (removing duplicates, etc) into #1 (because my computer is set up for multiple users and I wanted all users to have access to all templates).