Here:[related topic] 1 they say that in YOLO actually the IoU (intersection over union) used twice:
1- during training to compare ground truth box to predicted box
2- during the usage of already trained YOLO network this technique is being used to eliminate overlapping boxes which include same object many times.
As far as I know eliminating overlapping boxes is being done by process called Non Maximum Suppression (NMS). Thus I wonder maybe the IOU is a part of a NMS process?