As the Title describes whenever I try and spawn a tornado in the Mountain or Stone shore biome it does not destroy any blocks, it works in other biomes but just not this one is this intended or is there a setting somewhere?

Yes, this is hardcoded into weather2. Any mountain biomes or biomes that are as high as a mountain will not be affected by tornados.

Not a bug. Just a very stupid feature. Do really hope Corosus removes this as it removes the purpose of the mod, especially for Minecraft servers with the mod installed.

I'm also experiencing this issue, help would be appreciated.

I believe it may be an intended feature, as it is a common myth that tornadoes cannot pass over mountains. The tornadoes also don't destroy blocks in the Mesa Plateau, Savannah Plateau and Shattered Savannah biomes.