Verified answer

the jack is a headphone signal and should never be used to AUX inputs as they use different signals this will result in any or all of:

faint sound/distorted sound/burn out of ipod/burn out of Audio system

then dock connector has ability via apple docks and Audio or video cable to give a proper phono output for audio systems..

the sound quality will be ever so slightly better on an ipod dock but it isnt enough to make a big difference