You just spent a load of money purchasing an "A" quality boat your have every right to expect it to be delivered without problems. If you wanted problems you could have purchased a lesser boat for a lot less money. So to your question you are not nitpicking, GW promotes themselves as number one in customer satisfaction????? Doesn't sound to satisfying to me!!!
As for the passive circulation in the live well, it is normal, at least it was on my Pursuit, I didn't order a live well on my 275 so I can't say for GW. That said it makes perfect sense to me that if the valve is open that water will flow while underway. When not in use it is always a good practice to close the valve, one less opportunity for water to enter the hull. As for the stain I would go absolutely ballistic on the dealer with a new boat, take photos and don't touch it, make the dealer and GW deal with it. Make them explain how they plan to address the issue before they do and then check out their solution to confirm you agree with the approach. If they can't fix it they owe you!!!! Water line, make the dealer come to the boat mark the water line with the boat in the water with full tanks of fuel and water and then they will have to take the boat out and repaint the water line. Engine issue, no clue but my blood pressure would be out of control if I was in your shoes. I guess that's why I have a heart condition.