To predict 3D curvature at a voxel position, you need to know the neighbors of that voxel, so it is expected that you cannot crop tightly to the region of interest but you need to add some padding (crop less). If you perform multiple iterations then you may need neighbors of neighbors, too, which means even wider thicker padding.
Therefore, it is expected that you need add padding (thick slice, larger around the region you are interested in. The more iterations you do, the larger padding is needed. 20 voxel padding on each slice does not seem excessive, so what you experience may be normal.