I presume running a national rail system is somewhat different from a railway for a single city. How good are the national rail systems in these countries?

Japan’s is the greatest in the world, for one.

They still don't make money off of being rail systems, they make money off of real-estate developments.

So, sure, you can have a rail system self-fund as long as you let it build whatever the fuck it wants at stations and funnel all the profits back into the train line.