I also hear a sound that I would describe as a soft clunk whenever the engine starts up again. It’s no more noticeable than the auto-start on my wife’s Mercedes. If I’m listening to the stereo, I can’t hear it at all.
Really, the only time it bothers me is when the engine goes off and it’s 100+ outside. The a/c blows a little less cooler, so I find myself disengaging the auto-start when I know I’m going to be in city traffic on a hot day. Otherwise, it’s not that noticeable to me.