If it's just a cosmetic, surface gelcoat issue and there aren't underlying structural problems, it should be a relatively easy fix, and their would be little concern for long term performance or durability. It sounds like they're trying to work on correcting that. Just because it wasn't perfect straight from the factory doesn't mean it can't be corrected. If there was a major wave in the surface or a hook in the hull that would be a different story.
As for the comment of overpaying by 5 grand, that's pretty much what happens most of the time with dealers in western ND, especially Bismarck. I personally know several people who have gone to South Dakota and Minnesota to purchase brand new boats because the dealers around here weren't close to competitive. That goes for other dealers that sell other brands besides just the one mentioned by the OP, although that one in particular is known for their high pricing.
The electronics thing sounds like a mess. I'm guessing there's more to the story than just "they did not install the electronics I wanted".