A TopicMapReference is a wrapper around a tm4j-Topicmap. Panckoucke uses TopicMapReferences instead of tm4j-Topicmaps for two reasons:
A TopicMapReference is returned to your application by several methods of the StoreManager interface. Other methods of this interface expect a TopicMapReference as a parameter.
Furthermore, TopicMapReference defines the method
public AMNode getAMNode() throws IllegalStateException;
This method returns you an AMNode that represents the underlying topicmap object. Thus the method serves as the connector between PanckouckeStore and the abstraction layer.
See the section about opening a topicmap for a complete example.