It is better to cook the stuffing separately and add it to the bird as you cook it. Yes, as long as the fruit is well washed. The rotten parts do not make you ill with food poisoning. The mold can produce a toxin that spreads to the food, so I don't recommend you eat this. It is because it happens so quickly with fruits that are warm and moist and the molds quickly grow.
Many forms are harmless.
It is found in the dirt and in water and digestive tracts of many mammals and even humans. The ones that make us sick tend to be associated with raw meat, poultry and can be easily dealt with by making sure the meat is cooked to 160 degrees, making sure your hands are washed thoroughly and making sure that there is no opportunity that foods associate with other kinds of foods. For example, clean your cutting board after using it if you are going to start handling other kinds of foods. It should not be kept out of the refrigerator for more than two hours. Then you leave the food poisoning bacteria on your sink and rags and from there they can be transferred to food preparing surfaces and your hands.