I know this is an entirely experimental feature, but I had to try it because we used it often in our multi-player worlds. When I use an older version of MC to create my preset, and then export the file in the latest version, certain settings such as minheight and maxheight of certain blocks are not respected.
Steps to reproduce
Create single player world
Import worldgen settings from a preset world (attached)
Play world
Teleport to 0 80 0 in creative mode
Expected results: diorite, andesite, and granite do not appear above level 59
Actual results: diorite, andesite, and granite appear above level 59
Other settings in the export are modified as well, but not as clearly demonstrated, so I use the above 3 blocks as an example.
I don't think that's how that works... The new custom world settings are totally different from what existed in 1.12 and under. You do have a lot of control over every aspect of worldgen, but you have to respect the new grammar for it to work. Check out slicedlime's video series. The easiest way to remove the stone ores would be to create a datapack that replaces them with stone in the worldgen/configured_feature folder.