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The default stencils are inside the OmniGraffle application package. I suspect that you could move them from there into your (organised) Application Support folder. However, I don't know if that will damage OmniGraffle in any way so I would back it up first and e.g. label the current third party stencils in your App Supp folder so that you can easily identify the default stencils you move there to be able to remove them if you need to.

Problem is, if it works - every time there is an update to OmniGraffle, you will have to go through the same process.