Thanks for the report, I tried to auto-generated about 800 worlds and none of them have a flooded cave. :(
Could it be that you installed a mod which changed the default world generation?

But anyways I solved the issue by adding a tent to the mining base as spawn which has some hidden sponges to make sure you are not drowning.

The new mining base will be part of the next release in the next few days.
To reset your mining dimension, just delete the mining dimension folder dimensions/mining_dimension.