Opening any door primes the fuel pump. And when turning off the vehicle there's all sorts of modules that go to sleep at various times and make all sorts of noises. Totally normal.
Yes, it's a dealer installed option, but it's on the main factory sticker (not the little dealer add-on one), so it's known which particular trucks will have the black-out package from the start, so they could have the black z71 fender emblem staged on the line where they get applied. Seems simple enough.