The issue I think is the way the two types of path (elevated, flat) act with the terrain. You can see this from the straight edge of the terrain clipping through between the two path types.
The flat one is simple. Whatever terrain is below - Stick to it like paint.
With elevated paths, it can't do that or the whole section will stick to the terrain. It can't act as both a flat and elevated path. Which it really needs to do. Those sections need a way of detecting the terrain and half sticking to it and half not...