Currently Fill down will fill every air block from the location clicked down to y=0 with the selected material.

The default behavior of this brush should be modified to fill down to the first non-air block. So that air pockets beneath the land you are working above are not filled with your material. A flag should also be added to enable the old 'fill down to bedrock' behavior.

Seems like something we should do.
Currently working on the new code basis though.
Maybe somebody else could patch that and send in a PR? Would be highly appreciated.