Unless the downspout sticks out past the back of your swim platform the bubbles will still float straight up.
Since you want the bubbles to be past your rider when you are driving, it is better to have the FAE as deep into the water as possible, as opposed to having if as far behind the transom of the boat as possible.
My FAE is installed, but not tested yet!! How much quieter would you estimate the boat is? Have you tried to start it when it's already on yet?