Rail networks have massive network effects. Might be best to let the market not have that one. What with the huge risk of regulatory capture and all.
The most efficient freight railways in the world are probably in the USA, and passengers in Japan. Both private vertically integrated things, with the one company owning both rails and trains. But yeah, massive potential for problems as well.
I don't really have a good solution. I'd guess the best industry structure is just "it depends", nothing that is superior to other ways of doing it in all circumstances..
As a user of transit I mostly don't have to care about this, but I ended up calling three companies when I lost something on the way home.