Not sure if that is a bug or feature, but when you set "random=true" all the custom files (loot, spawners, etc.) are completely ignored.

I would love to use the variety that comes with random dungeons, but still would need my settings (loot & spawners)

RoguelikeDungeons-1.12.2-1.8.0.jar
Forge 1.12.2-14.23.1.2590