The current tunneling system is fine, but could use some improvements in the forms of unique mutators and control options.

An option to fill in a tunnel or remove a tunnel exit

The ability for party members to follow you into and out of tunnels for massive escapes

No tunnel discovery. This one's self explanatory, staff will never discover or remove your tunnels

Prison map. This mutator would allow you to toggle your view at any time between surface and tunnels. This would allow you to scope out the area above you or to plan your tunnels from the surface

Ground durability. This already appears to be slightly in the game, but could use some improvements. Basically, just add 4 tiers of durability: dirt (soft), rock (hard), metal (very hard), and foundation (also very hard). Dirt would be any ground that has not been built on, rock would be areas with just walls, metal would be pipes, and foundation would be any area with walls with foundation beneath them.

Specialized tools. This mutator would have no effect unless the previous one is active. This would make different digging tools better with different strengths. Shovels, spoons, etc would be good against dirt and bad against everything else, hammers, pickaxes, etc would be good against stone and bad against everything else, axes, knives, etc would be good against metal and bad against everything else, drills would be good against foundation and bad against everything else.

Sub tunnels. This mutator would allow you to dig tunnels beneath your first layer of tunnels. If a tunnel is discovered, only the first layer of tunnels will be filled in