Hey TFP I have solved underground bases.
My solution is both brutally punishing and requires a minimum amount of work yet will solve your problem of big underground bases.
I'll be happy to share with you.
Trapped monster roaches/ scorpions / ants in rocks. It can be a very low % that increases as you get to bedrock.
Give them a very small chance of spawining when breaking a piece of stone. As you go deeper the chance gets higher without being crazy.
This would make players think twice about underground bases being super easy and safe. Yet still reward the player after their hard work.
But wouldn't be terrible to try to code.
Thoughts any of TFP???