You can actually configure this information both places - in the Ant subtask or a hibernate.properties file. It doesn't look like the subtask supports all of the properties (yet?).
I actually still keep the property information in a seperate file, like you described. Here is a snippet of what that would look like:
SessionFactory sessionFactory = null;
Properties properties = SessionFactoryFactory.getPropertyCache();
sessionFactory = SessionFactoryFactory.getSessionFactory();
Basically, you get a hanlde to the Factory's properties, and then load your properties from the file. There may be a more elegant way, but this works for me.