In my setup the cuts even out the terrain, so they 'bridge'. Where the terrain dips, the cuts go 'up'. It could be otherwise, perhaps. But you often have these areas in the real world where they have thrown up a lot of ground for a railway track, and dug it up somewhere else. But you cannot have a very steep or rough terrain, or it'll be too contrived, depending on the smoothness of the valley, that is. I add some roughness later, after making the valleys, or cuts. The thing is that a bridge would be possible (YES, I'll be your God!), if you locally add some (well, a lot of) lateral displacement, and keep it at bay with a simple shape mask (perhaps triangular or so). Do so on the other side of a valley, the other way and hopefully the bridge ends will meet.....
About following slopes. If it would be possible to use the same PF for terrain and warping of the line and lay out the line kind of along the valley edges, perhaps.... but then it would be harder to flatten that area, that's easier of course if the line goes perpendicular to the main terrain.