I think we're overlooking the fact here a finished product is filtered and suspended in solvents such as BA which is a bacteriostatic and helps keep the product "sterile".
Yes, infections can occur during pinning..As other point out they are relatively rare. From a statistical odds perspective; is it's more likely that infection was cause by production being without a laminar hood (but otherwise hygienic environment) or poor injection prep/technique by the user? Many users get complacent and do not clean the injection site prior to pinning... As you said, many bugs exists on our skin fauna...
I'm not saying contamination isn't an issue when replacing the stopper.... I'm highlighting that you can mitigate that risk sufficiently with a clean & disinfected workspace and good hygiene (use of proper skin scrubs, impervious apron, sterile gloves, hair net or containment if really necessary) To be honest for a quick procedure like changing a single stopper some sterile gloves would probably be sufficient.
All these pages talking about use of laminar hoods..very little on safe injection technique...my point about missing the bigger picture