I find my self importing the solved mesh from each chunk into a 3d application like maya and manually transforming it to match chunks.
I do that when I dont have enough cross point cloud information for it to align using the align chunk by point cloud or when i find the align by markers slightly off. It just seems alot easier and in most cases quicker. But unfortantly by doing this i can't either build mesh as a whole or build my textures as a whole.
I think it would be cool to have a chunk transform scale and rotate tool built in!