Then digging out the tunnels will give lots of diamonds, lapis and gold. The lines will require a lot of gold to make.
Having them right under the people transport rails would conflict with the points where the rails go down to cross other lines, like just east and west of the central station.
Also, the resources won't be stored at the stations, but at the public storages, I think. The public storage in Spawntown should be extended all the way down to bedrock-area. Hmm.
Detaching them from the people transport will also make it possible to make the routes more direct. I also think they would also have to go only between two specific stations.
in addition, because the original rail lines already set up, it is easy to establish the new storage lines simply by digging down 3 blocks! the 15 block y requirement renders this impractical.
But when you dig the lines out, you dig horizontally. It'd be a waste of time to dig up all the old rails/torches and then place back the blocks which were there to make rails below them.
They could also be at y = 40 or something, I'm not sure yet.