Building only every second track works by script, then you can add the inner track by hand.
I am quite sure TpF doesn't create the right tunnel entrance when building with a construction script and this creates a terrain collision. I am not sure how I could tell the tunnel edge to create the 3 parts portal. Creating a tunnel portal without models crashes the game when loading, so this isn't an option...
-edit-
If both edgeList don't connect this is the result: