I would not be happy with that, at all. I would prefer a B&W anyway, like I did on my last two trucks, but I went with the factory prep thinking you can't beat a factory install. Now you've got me worried.
Anyway, I'd first make the dealer test fit a goose ball, and fiver hitch, just for your knowledge, and short term use. Then, I'd be seeking an answer as to whether the holes in the bed are off, or if the pucks and gooseneck are mounted incorrectly on the frame. That is some pizz-poor workmanship right there. They need to make it right.