YOLOV3 - generateTargets function example does not follow YOLOV3 article?

https://arxiv.org/pdf/1804.02767.pdf

In the '2.1. Bounding Box Prediction' section of YOLOV3 article it is stated:

“If the bounding box prior is not the best but does overlap a ground truth object by more than some threshold we ignore the prediction, following [17].”

The IOU should be calculated between the bounding box prior and the ground truth.

In MATLAB the generateTargets function example:

https://www.mathworks.com/help/vision/ug/object-detection-using-yolo-v3-deep-learning.html

% Get the IOU of predictions with groundtruth.

iou = AMTrainYolo3.getMaxIOUPredictedWithGroundTruth(bx,by,bw,bh,groundTruth);

% Donot penalize the predictions which has iou greater than penalt threshold.

confMask(iou > penaltyThreshold) = 0;

The IOU is calculated between the predictions and the ground truth.

What am I missing?