Does anyone know what causes the head seams in NV? The problem looks to be entirely fixed in Skyrim, but how did they do it?

Well in Skyrim most of the body/body texture mods come with a facial texture as well so they looks fit together and significantly reduce the neck seam's visibility. Plus there's this tool from the creator of CBBE body called Tex Blend and it works magic with a few clicks.

Body types in FNV doesn't cover face's textures, only mods that change head meshes like Fallout Characters Overhaul do and it uses a different set of texture than all of the other popular body types as well.