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If you want to be sure Omni sees your question, you need to send it to them via Help->Send Feedback or email to omnigraffle@omnigroup.com. Posting it on the forum does not send it to any particular Omni employee, and there is no guarantee that anyone will see it, much less respond or do something about it.

If you want your document name to not have a .graffle extension, why not save it without the extension?