Dark feature processing can be used to modify diagram data as well as business data through existing Graphiti features, without the need to have any Graphiti editor open.
You just have to create the suitable diagram type provider (DTP) and feature provider combination for the diagram to be modified. The service class ExtensionManager provides some useful methods: createDiagramTypeProvider(IDiagram) can be called to receive a DTP loaded with all the infrastructure to process your existing features. But keep in mind that these features can not show any kind of UI because there is no real visible editor running.
So eventually you have to prepare your features to fit that needs.