Structures not generating properly in other dimensions

My mod adds a new structure to both the Nether and the End. 

The Nether structure always generates on the bedrock roof. A proposed fix in another forum topic was to set it as the "underground" generation type. This works with features but not structures.

The End structure always generates at the bottom of the end and barely crosses the build minimum, cutting the floor off.

Having these generate as features instead of structures would most likely not work as A) I want them to have terrain adaptation and B) I have tried generating a large structure as a feature before, only for it to get cut off.

How do I fix this?