There is no way to configure the Configuration before it is used to create the SessionFactory.
I ran in to this problem because I need to override the connection url, user and password properties in test cases (so that an in-memory HSQLDB database can be used). I am sure that there will be other scenarios where properties will need to be overriden at run time,
Access to the Configuration object might not be sensible. An alternative would be the ability to provide names and values that are then set in the Configuration before SessionFactory creation.