(I haven't used any of these features, so the following is just a guess)
In your assertion, you are comparing two *Point instances*. The SQLAlchemy comparator_factory mechanism has not made any changes to the Point class itself, and Point doesn't define __gt__, hence your TypeError.
The point of the comparator_factory is to add class-level behaviour when you are building SQL expressions. In this case, you could write a query like this:
query = dbsession.query(Vertex).filter(Vertex.start > Point(2, 2))
Hope that helps,
Simon