I dont think it will be possible to add tunnels as a feature, the way the game generates and maintains the land and water areas makes for quicker drawing but it does not lend itself to defining anything under the land... it basically just records the surface of the land, and the level of the water.
Underground items are seperate objects in the database.

You can build small caves if you dig under a large rock (the rock object, not rocky ground), but thats about it, that and basements under your house, with the floor as the roof (note floor tiles do not count as a roof when it calculates sheltered status).