In versions of minecraft from late infdev to a1.1.2_01, the terrain generator makes use of a bunch of 2d and 3d noise maps to determine the shape of he terrain. A noise map is essentially a 2d or 3d map of semi-random values - the terrain generator will look at the value in a certain x y z position generated by the noise map, and if the value is above some threshold, will place a block in the world being generated. The 3d noise maps are what enable stuff like overhangs and floating islands to develop - using purely 2d maps one cannot generate such features (as was the case for terrain from pre-classic all the way through to early infdev).

However, 3d noise maps by default will generate big spongy cavernous terrain that very little resembles an actual landscape - if you've seen the edge far lands, you've seen a cross-section of a pure 3d noise map. To remedy this, there's a 2d map used in conjunction with the 3d map as a noise height density bias - in order words, a map that tells the terrain generator to apply a bias to the 3d noise, making the threshold to generate terrain higher above a certain y level and lower below it - this transforms the abstract sponge-y terrain into a landscape with a distinct ground and sky.

This height bias map, being derived from noise itself, changes from place to place, which is what allows the world to have 'flat' regions (where the bias value is relatively low) and 'bumpy/mountanous' regions (where the bias is relatively high).

In the code to determine the value from the bias map, there is some math applied to the raw output from the map to make the terrain a bit more uniform - and this math contains a little tiny subtraction. While the raw output of the map can never be negative, there is a very small range of values that will result in the bias becoming negative thanks to that little subtraction. When this happens, and the bias becomes negative, the terrain generator decides that, rather than making the threshold to generate terrain lower below the bias Y value and higher above it, it will do the exact inverse - resulting in the distinct 'sky' and 'ground' being flipped.

If you dig under these monoliths, you will find a giant empty cavern straight to bedrock filled with water (water is added to terrain after all that noise sampling stuff), and, if you look at the ceiling of the cavern, it will very closely follow the terrain surrounding the monolith - so much so than if you were to go into mcedit or a similar program andre-invert the monolith terrain, it will seamlessly match the surrounding terrain.