AudioCore is doing the transcoding based on the settings in the Audio MIDI Setup. Keep in mind that EVERYTHING will be either up sampled or downsampled based on the setting. You either need a third party driver for an external DAC or another piece of software such as Pure Magic or Decible.Afaik iTunes is not trancoding (which would be required of course to modify the source). I can't guarantee it but some folks that should know tell me thats the case.
This is why I stopped using my Apple TV for music. I have a lot of hi-res music files (24/96kHz and above) and hated to think that I was not getting my money worth by having the Apple TV down sampling.The response I got over at AVS indicates that Apple TV 2 would convert my 16/44.1 ALAC files to 48 khz. I guess there is some debate as to whether or not this affects the sound quality. Thread here if you're interested.
Hammie's set up is a lot more refined that mine is. I ditched my Anthem pre/pro and amp about 2 years ago and have been using a Denon 4810 as my AVR. All of my sources connect to it via HDMI and then HDMI out to my plasma. I really was set on selling my mini since it rarely gets used for anything except some ALAC playback through iTunes maybe 1-2x a month. Now I'm not so sure if I'll sell it.