I would expect this breaks down to:
Plus fiberglass work
Plus repainting the entire transom (rather than trying to blend)
Plus repainting the name on the transom
Plus trying not to work on the gray side of the hull.
On a car, at high urban prices, a $400 repair like redoing a quarter panel. Plus the price of the haul.
Even adding a boatyard penalty surcharge...$1300 sounds high. My only question is will your $300-400 yard guarantee to make the repair *invisible* or will they simply "try to match it" when they feather in the paint? Some shops are real good at that, others just don't even try. (Be glad they aren't planning the entire hull side with it!)