You mention the neck/body junction, but I don't see a photo of that joint. Perhaps I am not understanding the nature of the problem. Is the problem only with the binding, or is there a more structural issue with the neck joint?
While I personally would not have an issue with the offcenter dots, it clearly is a fault. Your best recourse is to deal with the seller. If he is an authorized dealer, he should act as the bridge between you and the factory. Having modified the guitar with the Bigsby may present a problem.
Changing the binding on the neck would be one way to remedy the situation, and I fear that it could result in more visible flaws. The dots are knocked in by hand, so the dot could be drilled out by hand, filled and redrilled for the new dot.