Hi Andreas,
I apologize again for the time it took me to get back to you. I agree with you these lines are confusing, and I will bring this up at our next ISSM meeting, they are there to just provide some default thermal boundary conditions when the model is extruded. In practice, boundary conditions for the thermal model have to be defined AFTER extrusions since we need to know what vertices are on the surface, so we never noticed that problem.
I hope this helps
Mathieu