Basically, have tracks trains can go both ways on, which will save a LOT of space. It could probably be a different (maybe researchable?) kind of track.

Trains already go both ways on tracks - after reaching the end of a track, a train will make a return journey by travelling on the underside of the track in the opposite direction.
But there is indeed a gap in functionality for interacting with trains travelling on the underside of tracks.
Perhaps this could be filled by researchable variants of train stops, loaders, and unloaders that interact with trains on the underside of the track?
Having stops/loaders, etc. upside down under tracks makes no sense with the game’s current mechanics. It would require a -1 space level, or some way to view the underside of a track (either the trains are viewed travelling upside down, or you would need to rotate the camera upside down).
It would be much more intuitive to simply have a rail upgrade that is essentially a double track with opposing directions (like a real train network).