Okay. So ultimately I'm going to have to tweak the ground to accommodate the entrance. I'll try to reuse rocks to help obscure things rather than disabling them and make sure not to add too many new items due to LOD - would copying items and using those require a LOD redo? Will disabling a large mountain be the same as if I pushed it below the ground or is disabling better?
LOD was generated as the world looked pre-release when Bethesda were making the game. Anything that was there at the time is in the LOD we have. Think of it as a picture, it's static and doesn't change. So if you add a new huge rock, it won't be visible in LOD, because it wasn't there when the LOD was generated, regardless of it it's brand new or duplicated. Same applies to if you delete or move an existing object, it will stay in its old position in LOD and won't move or disappear until you get within loading distance. Landscape is a little different, LOD for landscape is actually a little bit below ground of the real landscape. If you dip the landscape down too far, the player will actually see the LOD for that landscape, which is obviously bad. However the same applies to that if you make a massive gorge or mountain, it won't be visible and will just pop-up when you get close.
Generating LOD is a pain in the [censored], and modders tend to stay away from it, so therefore it's better to just change as little as possible.