Hi Rogelio
I have not seen the code of BN, but those values certainly look like thresholds of the data, to set valid samples, and nothing else.
Also, there seems to be no statistical rejection, to avoid stars for example. The process is just confident that you selected a good reference, where the background dominates the statistics (the peak of the histogram is a good approximation to the background mean value, and so is the median of the reference).
You may decrease that value to avoid "contamination" of the sample, and let the median to be closer to the peak, but I would say that for background neutralization purposes, it is not critical.