if you take your time and just doing spot welds not to bad. but id say your going to see some discoloration at least. You may try a fan on the hydro turf side to help cool it faster so it isn't as bad.
My bet is burnt up hydroturf. If you pre chill the deck with water, then you still have to get the aluminum up to welding temp. That means more amps or more time, and the way aluminum moves heat, you are gonna have a big burnt spot instead of a little one. You won't want to quench the weld with cool water when you get done, or it could end with a cracked weld. I think your best bet would be to start with a warm work piece, and MAYBE cool your tack welds with a towel soaked in hot water. Easiest fix would be a new Wet Sounds system so you won't hear the rattles.