This is a wild guess on my part buuuuut.....
Most likely this is the dock outputting "line level" which is very close to, but not exactly the same as, "headphone level". The difference is in output level and impedance. Long and short of it is, this output was designed with the idea in mind that you'd likely be plugging it into a stereo or something of that nature, and the output is "cleaner" than sending headphone level into a stereo.
Notice that when you take something like the phone or an ipod directly, and go into a stereo, sometimes you have to set the phones volume at something like 75% so that the stereo doesn't sound distorted?
Or I could be completely wrong.