In the mathematical sense we have trees, without cross-links, and graphs with cross-links. An EMF model with only containment relationships is a tree. As soon as you introduce non-containment references, an EMF model can be a graph.
We normally use the term model transformation for transformation of models since at the Java-text / Ecore-tree / Xtext-text / Emfatic-text / OCLinEcore-text we ignore the graphical picture.
In contrast there is a strong graph transformation community who concentrate on the much stronger discipline associated with the visual representation and patterns. UML, Ecore Tools and the Henshin and UMLX exploit the strong model/graph equivalence.
Your original quote therefore highlights a statement that while factually correct is easily over-read and so confusing; much better if it has said "transformation of graphs".