My guess is this is dealer driven, not Yamaha driven. Yamaha is standing behind the bolts today. I would try another dealer. Have them show you where you hit anything! If you did, there would be damage to more than a broken cable. This is outrageous! Go over the head of whoever your talking to...this is a dealer issue, they are the ones that submit and get claims handled.
I just dropped my boat off at Phil Dill Boats and I didn't even buy from them this time, they are getting ALL of my warranty work approved by Yamaha. If they go through the proper channels and you have proper evidence of a warranty issue, it gets approved. So my recommendation to you, is to go to the service manager and get him to see the importance of taking this to Yamaha. The bolts are an issue, especially on your boat! Spider cracks however, are cosmetic, and if they are not stress related during assembly, you may have a battle there. Upholstery they will cover, if it is apparent that it is a manufacture error. Even some spider cracking they will cover.
Let me explain the difference in dealers. At PD, when a boat comes in, they fix any spider cracking they see, and they buff any damage from the worthless bow roller...then they replace it with a non marring roller!!! This is quality dealer character doing what quality dealers do. They don't go the extra mile because you blow a gasket, they do it because that is their business philosophy and the way they treat their customers. And I am sure someone could have a bad experience there because 100% isn't attainable by anyone...but they would do their damnedest to make it right. So if your dealer isn't cutting it, find one that will and then give them your patronage.