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.