You can increase the depth of the ground with the depth base size but you can't change the way caves generate without mods unless you just want all or none - by far the biggest omission from Customized, given the game:
Any change in the value of 1 corresponds to a variation of the base height by 8 levels. The value 0 can not be set because of the base amount at least still the bedrock level must be generated. The default value of 8.5 corresponds to the base height of 68, which is slightly above sea level (level 63).
Caves do not even generate (start at, some do go higher but most caves do not have much vertical variation) above y=126 and the majority are well below the default sea level:
This is even worse for mineshafts, none above y=54 except in mesas, and then still not much above sea level, and ravines have a similar distribution as caves but between layers 20-66 (ceiling up to y=88 for the largest ravines as this is their center point and they are up to 45 blocks deep). Dungeons can generate up to the height limit but require an underground air pocket to generate so in practice they are mostly below sea level.
Note that they say this about the upper/lower limit scales but it is incorrect; they have nothing to do with cave generation (you can make hollow pockets appear, as sometimes seen in mountains, but they are not the same and will have grass/dirt/sand/etc lining their floors and be filled with water if below sea level):
Make terrain more solid/riddled with holes depending on how close the values are to the lower limit scale values. Note however, that it is used in cave/cavern generation, and so setting them far apart with caves/caverns turned off doesn't give you holed terrain.
I made my own mods which increased the ground depth to 128 or 192 layers (in a different manner which kept surface terrain features exactly the same as a default world) and scaled up cave, ravine, and mineshaft generation to fit, including making caves and ravines much larger/deeper but I only made it for 1.6, and other (more current) mods that let you alter cave generation do not really let you change much.
There are also some other issues, such as the level at which certain structures generate at (ocean monuments and desert temples will be underground).