I'll have had my Mossberg, 5 years this september. I've been through many changes with her from stocks to optics, paint to stained wood and various configurations in between... But when all is said and done, she goes Boom! And as long as I'm happy with it, that's all that really matters.
I don't know about the other issues, but I have seen Mossberg 500 barrels with the rib mounting marks. For the price of a Mossberg I don't expect the polished perfection of a Perazzi, but visible dents in the bore was too much for me when I saw it on my new turkey gun. My LGS swapped it for a better barrel from another gun in stock (I'm a really good customer there) but I don't know what they did with it.
I'd contact the store and/or Mossberg and see what they have to say. You don't get to complain until you've given them a chance to make it right. Let us know what they say.