A dealership trying to screw a customer over by denying a warranty claim and coming back at you with an outrageous bill full of unrelated/uncessary stuff. How sadly common. Been there myself with another issue.
Oh and it's also common practice for them (and BMW in general) to say that they "have never heard" or seen a common issue before. Eg: vanos blowing up on the E46 M3s.
Anyhow, what you need to do is put up a fight and escalate to BMW NA corporate. In this particular case I would really be surprised if they did not take care of you, given how new and low mileage the car is.
Your other option -if your time is precious and you don't want to fight- is to just bring your car to the nearest reputable independent BMW repair shop and have them extract the broken bolt and install a new one. That shouldn't be more than ~a couple hours of labor.
Last but not least: the chips on differential = just road stuff, rocks etc when driving. Same stuff that chips the paint off the bumper. Normal.
Good luck and let us know how things play out!