I have an apple tv connected to my tv. I just purchases a universal dock to play music through a receiver. The TV does not go through the receiver. The apple tv and the dock are very close on the shelf. The apple tv and dock have the exact same remote, but they both want to control the tv and not the dock.
I understand the preferred set up would have been to hook all up to the receiver (and wouldn't need the dock) but it is an old receiver that couldn't handle the Tv stuff.