The scripts don't have any tools for smoothing track bumps. Only thing I can think of is that I don't look at it as separating materials. I look at it as separating meshes, using Blender's Edit Mode:Mesh:Separate By Material ('by selection' works also). Using that tool has never left any gaps or bumps -- unless you move the mesh from its original position after separation. Beyond that I just rebuild track sections until I get what I'm looking for. The folks over in the Modding forum probably have more info about fixing bumps than I have, because I'm primarily focused on the scripts.