I don't claim golden ears, though I hear you claim shit for brains.
Nor did I actually say that you did. As for the rest, not as far as I know, but I do not claim to remember everything I have written, and haven't looked in there lately. Maybe you're right.
The (safety) ground should be a pass-through; I am wondering if the installer used adequate ground strapping. But that should not cause the total collapse of sound the way you (if it is really you) described. I did not hear a dramatic difference in sound before and after our Generac was installed. I would love to hear the root cause if you find it and what really happened. What I do believe is that there is a rational explanation. Given the way power systems work, I would suspect the safety ground connection more than the line/neutral connection.
I am not sure you can legally bypass the transfer switch; that could cause load-dumping back to the grid if the generator should cut on, and "interesting" results when power returns if the generator is basically hard-wired to the incoming power. It also might not isolate the cause without trying several things on all three wires (line, neutral, safety ground) to your listening room.