Three-dimensional (3D) depth imaging systems and methods are disclosed for dynamic container auto-configuration. A 3D-depth camera captures 3D image data of a shipping container located in a predefined search space during a shipping container loading session. An auto-configuration application determines a representative container point cloud and (a) loads an initial pre-configuration file that defines a digital bounding box having dimensions representative of the predefined search space and an initial front board area; (b) applies the digital bounding box to the container point cloud to remove front board interference data from the container point cloud based on the initial front board area; (c) generates a refined front board area based on the shipping container type; (d) generates an adjusted digital bounding box based on the refined front board area; and (e) generates an auto-configuration result comprising the adjusted digital bounding box containing at least a portion of the container point cloud.