They aren't stupid, but they are hoping that you are, and you aren't...
They didn't replace the valves, period, they had no reason to replace them. They can get you some old valves from the machine shop, but they aren't yours. Why would your valves be in the "parts area", they should be at the machine shop.
They had no reason to machine the head, the machinist said it wasn't warped, they may have cleaned the surface up with a light grind, but I doubt it.
They are just trying to justify the expense.
They probably did a decent job, remember the mechanic doing the work is not the guy doing the bill. Hopefully the mechanic has some integrity and isn't just after the almighty greenback. I feel for you, the dealership sucks and I would never go back to them again..