In the image below the sail train travels from station A to station B over a curved rail. The difference in height helps the train accelerate and allows us to store some of the breaking energy.
The image is intended to inspire the reader to explore the concept of the breaking vs acceleration energy. Accelerating doesn't cost energy, the only energy lost is friction from moving and losses from storage of energy.
An obvious downside of using height with a sailtrain is that it could be rather large therefor hard to build a tunnel for. Alto it doesn't need to be as big if we can find a way to guide the wind into a tunnel. Large screens by the track could 'shape' the wind to be more useful. This does presents challenges when using the rails in 2 directions but I imagine tremendous acceleration can be achieved with relatively small sails.
The rails could run in a circle with it's stations 40 meters above it's deepest point.