YOLOV3 - generateTargets function example does not follow YOLOV3 article?

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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:
% 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?

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