Yes.
It is possible using the terrain editor tool, part of SimCity4 Rush Hour and not a custom download.
Just use raise your terrain tool, and using the leveling tool create/drag yourself a raised tunnel. Place the train tracks into the end side of the hill and out the other side. It only goes in straight lines. This tecnique is also helpful for crossing monorail and elevated highway. For City wide use however, it is easier to raise the terrain of the entire city, and lower the terrain at intersections/stations.
Carl
https://www.simtropolis.com/idealbb/files//ScreenShot118a1.JPG align=baseline>
