What they say is

Cacao beans are grown on family farms, so there are literally infinite possibilities between harvest and bagging where they can be exposed to pathogens from living creatures or humans.

Even during normal fermentation where the beans can achieve a temperature as high as 125°F (51.7°C) that temperature is still not high enough to kill all the bacteria. We’re not being critical of the farmers – it’s just a fact of life on a farm that they can’t control all the variables that may introduce pathogens into their crops.

So a chocolate manufacturer or artisan chocolate maker must assume that the bagged beans arriving at their loading dock are contaminated with some, if not all, of the following: Salmonella, Listeria, E. Coli and Staphylococcus.

But it's not clear why that would apply to cacao beans and not to say, lettuce, which everyone eats raw.