The bug

Strongholds do not generate in certain customized worlds despite /locate saying otherwise. At first, I thought it was caused by blackstone as default block. Later, it turned out that it was not generating at all. Then, I thought it might be caused by effects being set to nether. Even with overworld effects there was no stronghold.

How to reproduce

1. Download the 210612.json file
2. Import it to a new creative world
3. Use /locate stronghold
4. Teleport there
5. Set your game to spectator mode
6. Fly down
   →  No actual stronghold, but the message from /locate still says that there is a stronghold

Might be caused by the biome distribution having nether biomes. The best possible fix might be to make strongholds generation independent on biomes, but on the worldgen import.