The bug

The ender dragon fight is hardcoded into the dimension type preset for the end. If you manually set all of the type values instead of using a preset, there's no way to make the ender dragon fight appear. This seems like it might be an oversight, since in the source code the flag for the ender dragon fight appears right next to all of the other flags which are configurable through JSON, even though the ender dragon fight isn't.

This is an issue because it makes it very difficult to customize the end without essentially breaking the game. Changing any of the type settings in the end requires not using a preset, which means that changing any of these settings will automatically remove the dragon fight from the world.

How to reproduce

Use the mcDefaultTest.json file attached to generate a world. This JSON file expands the dimension type field for each dimension and the noise generator settings field for the overworld with the game's default settings. Use "/setblock ~ ~ ~ minecraft:end_portal" to place an end portal at your current position and go to the end. Here, there is no ender dragon.