Specific structures do not generate in superflat worlds, even when specified in the superflat preset.

To reproduce:

• Create a superflat world, using a preset that specifies any combination of the following structures:
  Stronghold, Mineshaft, Ruined Portal, Nether Fortress, Bastion Remnant, Outpost, End City, or a Woodland Mansion

• Explore the world or use /locate. There is an absence of any structures, excluding villages if specified in the preset.

Eyes of ender do not work in a world which specifies strongholds. The locate command fails to find any of the above structures. Villages generate without error.