Let me post here the advised work-flow from the help desk correspondence as that might help also to other users.
"RailClone surface tools are a little limited at the moment. Rather than follow the polygons or the UVs like a paneling tool, in RailClone geometry is projected along the RC object's local Z axis until it hits the surface's geometry. This means that it only works well when the face normal points towards the RC object. Any polys with faces that point away or overlap will not work.
There are multiple possible approaches:
You could perhaps get around it by spitting the surface and using several RC objects with different orientations but I don't think it would be easy, or even possible to get them to align so that it looked like a seamless structure.
In some cases, like this one (I believe you have discussed with my colleague Paul), "slicing the surface" to get base splines does the job easily.
There are several similar ways how to get these splines from the surface - for example, by using the Boolean Compound Object in the Union Operand Parameters on your surface and another object composed by multiple planes (which can be made easily for example with the help of our free Clone modifier tool) - adding an Edit Spline modifier on the top the stack should do the trick.
Using Shapes > Section might be another possible option.
Another option might be to use the SlideKnit script in those difficult areas. This script allows you to flatten the surface, apply the high poly object and then morph the surface back to its original shape, deforming the geometry in the process. You can read more about it here: https://simonfuchs.wordpress.com/2014/08/17/tutorial-adding-detail-to-your-highpoly-objects-using-the-slideknit-script/
Also, it's possible to the Forest Pack plug-in in the UV surface mode - that would require accurately unwrapped surface."