Did you read this other thread that was linked from the earlier responses on this thread? You’re right that only one of the two boxes that overlap are included, but the other independent box containing the small white car on the right side of the image is eliminated because its confidence score is 0.26, which is below the 0.4 threshold.
In other words there are two ways to get eliminated here: because the box has a high IOU with another box with a higher confidence or the end result of the IOU elimination is a box below the overall confidence threshold.