It would be nice to be able to at least programmatically always Save on Close without the prompt so the check-in dialog will appear after the save(which the prompts can already be hidden).

Document.Save()
doesn't always catch everything and when
Inventor.CommandManager.ControlDefinitions["VaultCheckinTop"].Execute2(true)
is called it will throw this error

I have never had an issue with this check-in error when I save the document via the Save on Close dialog. I would like to be able to do that programmatically without having to simulate an ENTER key press in my code: See this forum post