Hi,
Yes, the rail lines need updating. It appears that some may have been done with PTv1 ideas (1 route with ways marked both forward and backward) and some with PTv2 ideas (separate routes and ways for each direction).  I have been working with the bus routes, but as there are thousands of them in NSW, so it remains a WIP. See PTNA for the status of the various rail/tram/ferry/bus routes and what is wrong about them.