The risk of rinsing is a very good point that I had also considered. I actually decided not to rinse the substrate post boiling for this experiment for that reason. I figured my sink head would almost certainly have some bacteria on it so I ended up boiling for 10 mins, and then took a small strainer that I had soaked in some 70% ethanol and dumped a sample into the strainer. Then I swabbed the center of the sample and moved forward with that. Still possibly could be contamination from the top of the pot while I was dumping it out or something similar, but I did the best I could to really just isolate the sample.
The only thing I can think of it that the clay is super porous which is kind of the selling point of it because it allows it to absorb a ton of water. So I'm wondering if those pours allow for bacteria or spores to sit safely away from the super lethal temperatures and gives them a chance to survive. I wonder if boiling for 20 mins or 30 mins would make an improvement, but at that point boiling for so long is almost just not worth it.