My thoughts are not as much about acidity but the chelating effects of humic substances. Certainly the insides of a tortoise are organic material. How about the mucus deposited with tortoise eggs whlie laying? Or the observation that most nests I've dug up contain some fecal matter the mother seems to deposit in the chamber? All could contribute to chelation and calcium mobilization as well as establishing microbes for gut flora when the hatchlings emerge. How much we change that balance when we artificially incubate is worth investigating.
In line with the quoted paragraph, I've been having poor hatch rates for my SA leopards. The breeder I bought them from also reported poor hatch rates with artificial incubation, and he let them incubate naturally in the ground. He reports "incubation" times of up to 18 months, because the eggs must undergo diapause and can't begin to develop until the summer heat kicks in after a winter underground. This year, I intend to leave all the eggs in the ground and cover each nest with an open mesh cage so that predators can't get to the eggs, and other females can't dig them up or disturb them to deposit their own eggs. Next spring, I will dig them all up and artificially incubate them. Best of both worlds. I'll leave a nest or two in the ground just out of curiosity.