The tunnel entrances use dighole (Scenery Type). These moves when merging. You can try and test, take any of your routes and merge Donner pass to it. you should see what happens.
I am creating in between baseboards, where there are height differences. The height of these 2 routes is at certain points the same height.
I brought over Mojave from TS12 to all the versions as they came out. The stand-alone route is perfect. I updated the track around the loop as it is currently in real life, with a longer dual track. I loaded a screen shot a while ago.