Yes, the default comparison method is by ID - this is why the default GUI states "matching by ID". Alternative comparison methods can be defined and added into the combo box, but you will have to define them programmatically.
Plugin org.eclipse.emf.diffmerge.ui.gmf provides an example of how to do that. You will essentially have to define your own IMatchPolicy, which associates every model element with an object that identifies it (qualified name for example). You may note that heuristic matching is not supported and is not intended to be, for trustworthiness reasons.
Don't hesitate to ask if you need more support. Could you tell a bit more about your use case?