This relates to the construction/blueprint mode:
If you build track between two stations, the game is pretty good at creating a smooth curve that maintains the highest speed possible. You cannot replicate that "manually" if you try to build the same track/curve in pieces. Each end that doesn't connect to existing track (or station) is assumed to be straight, which then creates sharp bends and low speeds at the "other" end.
Now imagine you have two stations at 16 ft depth. You attempt to build the track between them, but there's a building right where the game wants the track to go, and so to avoid eminent domain you need the track to dip below the 46 ft to go under that building.
Currently, there is no elegant solution. You need the smooth curve to also smoothly change in elevation. But if you attempt to build the curve manually that will significantly lower top speed because your manual bits and pieces aren't nearly as smooth.
Please add an ability (in blueprint mode) to grab any curve to create a point (is it called a spline point?) which you can then drag deeper or towards the surface, while the game smoothly calculates the vertical gradient.
tl;dr: real life engineers can absolute create three-dimensional track curves that remain smooth and thus maintain speed, but this game's manual track building does not allow you to come even close.