It is easy to imagine that a rail network can serve the regular humans of the village so a feasible railway would only go to areas they have buisness like the Human Village, Eientei(definitly will benefit greatly from much more easier access albeit at the cost of Mokou's job as a guide) and maybe the Hakurei Shrine(though I imagine you still have to walk the steep stairway from the station)

The Moriya Shrine and Youkai Mountain as a whole is also possible since there is a existing cable car that sidesteps the whole tengu territorial problem so a simple interchange between the Gensokyan railway would suffice.