This may be me misunderstanding something....however....
There doesn't seem to be a way to set TransitionFactories in either of the classes that use them (CloneableVertexGraphExplorerAlgorithm and TransitionFactoryImplicitGraph). The constructors don't accept these and the property is get only.
Again, it may be that my understanding of the expected functionality is flawed, but I don't see how either of these implementation classes can do anything really useful without being able to set a transition factory.
I can fix a copy for what I need - if you would like me to contribute any changes then let me know.