All true info about the chickens, and much of what you said is also USDA regulation. My company has USDA permits and these things are regularly inspected at my ranch. However, totally different animals, totally different type and amount of waste being generated, and a totally different housing situation. We aren't trying to maintain sterile conditions for these tiny little shelled reptiles. The amount of waste and type of waste generated by even a single chicken is exponentially more than what is generated by a little tortoise. The type of waste too is completely different. Also, since we soak our babies daily, almost no waste is deposited into the enclosure onto the substrate. Any that is deposited is easy to remove. Not like the more liquid chicken waste that squirts everywhere and gets into everything. A tortoise turd sits on top and waits for pick up.I could see that. A lot of what I know about animals, I have learned from keeping chickens. In chickens, anything in wood is bad. As far as equipment goes, you want plastic or metal, because they are easy to clean. Wood is a huge no no because wood is porous, and will retain microbes and water. So the poultry experts recommend painting any structure that is wood with something that repels moisture so that it can be easily and thoroughly cleaned. Rubber, seems to me like a product that is non-porous and easily cleaned. So I didn't think it would be too much of a stretch to apply the same principles to tortoises. I can see what you mean about how it could create films of bacteria on the surface of the rubber, but isn't it intriguing how it can be cleaned periodically?
Every animal species has different housing requirements. I don't house the dogs the same as the chickens, and I don't house the camel, the same as the kangaroo. I don't keep a fish only tank the same as a reef tank. I don't house lizards the same as snakes, and I don't house my roach colonies the same as my tortoises. Every species has individual requirements. Baby tortoises require a thick damp substrate that they can dig into, that resists bacterial and fungal growth, and that absorbs moisture so that it can slowly allow that moisture to evaporate and generate much needed humidity. Your rubber chip substrate misses two out of these three, and its also smelly and possibly toxic.