I think that VS is right - traditionally, if ground level railways were to be built through urban areas, they were built through lower density (poorer) areas, and the buildings demolished. There are no examples so far as I am aware of a ground level railway simply taking the course of an existing road, or roads but not buildings being demolished. The solution if one wants to build a railway through a town is to demolish buildings that get in the way. If one ends up leaving road connected spaces, buildings will grow back. This will accurately simulate the high cost of building through urban areas. This is why most railways avoided built up areas where they could. The same was true of canals.
The only examples of railways taking the course of roads are either underground or elevated railways (the latter being the American type, rather than the British type, of elevated railways: think of Chicago rather than South London). Cut and cover simulation was considered some time ago, but discarded on the basis that it was too tricky to implement, especially at corners. To simulate the early Underground railways, players should build ordinary rail tunnels, but put stations in a cutting.
The above applies to roads in cities. I have already changed the code so that roads between cities are not owned by the public player when generated, but are unowned and can be demolished by the player. There does need to be a rule for playing on the server, however, that the player must reconnect any road disconnected in such a fashion.
If, incidentally, there are bespoke conditions in which there is a compelling good cause to perform some surgery in a city and slightly alter the layout of the roads without demolishing buildings, a player can always request the public player to do the work. Genuinely good causes for such work are likely to be infrequent, however.