So I'm playing with both Oh the Biomes You'll Go and Betterend, and they both have biomes really close to this dungeon. I'm not sure which one of them is conflicting, but I'm pretty sure you can still easily set it so this thing can't spawn in the end no matter what.

This happens when the biomes aren't properly tagged. You should report this to the respective mods asking for their biomes to be tagged with the Biome Dictionary.