From an in-game standpoint, upgrading roads to have bridges (no costs of crossing rivers) has always been automatic. So to extend that to railroads has some continuity. While building railroads by hands makes intuitive sense and looks like logical action, one has to ask what benefit it really brings to gameplay. In civ2 when they reduced movement costs to zero, it was a clear gameplay benefit that required investment - see also airlifting units. In civ6 it seems to be just another reducement in movement cost (like bridges). On the other hand, upgrading them manually seems like tedious work and would require quite a lot of managing, even if they can minimize micromanagement (f.e. you most definitely would want the railroads on the same tiles as the roads, but you could imagine some short-cuts to mass-upgrading them). So yes, scrapping that (like the distinction between workers and workboats) in favour of less busy work in the later stages of the game seems logical. After all, each decision should matter, no?