Parts of Strongholds spawn above the ground if the Superflat "Overworld" preset is modified to contain fewer stone layers

All I've done was change the height of the stone layer from 59 to 5 in the "Overworld" preset when customizing the Superflat world type.
This had led to Abandoned Mineshafts and fragments of a Stronghold to spawn in mid-air, high above the ground. Apparently the Mineshafts are allowed to do that, but I haven't found anything on Strongholds, which also only spawn partially, without being connected - check the screenshots included.

The word seed is: 360212915417252929.