It's a Non-Mandatory element, so I guess if they determine that it does apply to you, you MUST comply with all parts of it and, unfortunately for us, their starting point was that it applies to everyone whether or not it actually does. We were able to demonstrate that our existing efforts and low risk processes adequately eliminate, or reduce to an acceptable level, the risk. I was interested to find that the stated pathogen in (SQF) 188.8.131.52, Bacillus, is not necessarily harmful, it is in fact present in most human digestive tracts naturally and does not typically survive paper making or our printing processes according to a 2015 study: Reference: "Health safety of food contact paper evaluated by in vitro toxicological methods", Adam Vavrouš, Marketa Dvorakova, Kristina Kejlova, Dagmar Jírová September 2015.
I do think that elements that are added are added to all codes without proper vetting to determine if they are applicable. I guess the "Shoot first and ask questions later" approach is applied here. Add them and then let the sites prove they are not needed, which is great until it costs someone their certification. It seems to be a somewhat lazy approach on SQF's part.
It may be that SQF have relented somewhat for Packaging rather than Food. Or maybe the number of Complaints has reached a tipping point.
Can compare to this recent Foodie one -
"Bacillus" is actually the genus. Bacillus spp. references an arbitrary species within the genus.
You are correct that not all Bacillus spp are pathogens. Curiously the parallel clause for food does not contain this sweeping generalisation.