The Nether is 128 Blocks Tall but the Map of the Nether is 256 Blocks Tall, there is 128 Blocks worth of dead space above the Nether, commonly used by professional players like a Superflat World on the Nether Roof. Same goes for Mystcraft Cave Worlds which have the same dead space atop but with Grass instead of Bedrock as the Ceiling.
Making use of that dead space should not hinder any other Mods at all. 