They damaged our new car installing the base plate

I think the shop is better than you think. At least they were honest and told you what they did. Many shops would have just fixed the line themselves (looks like an easy fix with hose and clamps) and you would have never even known it had happened. Once the line is replaced and there is no longer a hole , there should be absolutely no effect on your car at all. Same as drilling a hole in the radiator hose and then replacing it.