I know the CK isn't a full 3D editing program like 3DSMax, but wouldn't it be possible to add a Deform Modifier script to each local instance of a NIF that you could edit and set new locations for the vertices on the mesh (Not add or delete vertices, just move them around for that particular instance of the object only)

This would let you take two objects that don't quite fit together, but are close, and grab the edge vertices one at a time, and "Stitch" it to the edge of the neighboring piece. When the cell loads, it would first load the pieces as normal, then apply the Deform Modifier to move the vertices to where the person who edited each instance of an object wants them, and saves the resulting mesh as a temporary mesh (only exists while the player is in that cell) to render in place of the base Nif mesh.