Reproducing this bug:
1. Create a new world
2. Set it to Superflat and click Customize
3. Use the preset 'Bottomless Pit' from the Presets menu
4. You will see it has layers of grass, dirt and bedrock. These layers will also be there when you create the world.
Expected output:
Showing me no layers (or an air layer) and creating an empty world.
Bottomless pit means bottom layer is cobble.