It may be time to legislate the concept of "tunnel space". This would be similar to air space. In the US a property owner doesn't control the air above their land (subject to details). Maybe Congress should declare the Earth below say 100' as not controlled by the land owner and allocated by some new agency, say the Federal Crust Administration.

Remove all of this from state, county, and municipal jurisdiction. Centralize the rules. Local government will still be controlling the portals where it must surface and interact with the surface world.

This will have to merge with mineral rights, but the intersection of mass transit and mining is minimal.