Add me to the list of people seeing the same issue. I'm 99% sure it's the Apple TV not outputting in the correct formats and not an issue with people's AVR.
When set to "Auto" my AVR shows 7.1 PCM as the input if the source is surround sound (DD or DD+). If the source is stereo, then it switches to 2.0 PCM.
When set to Dolby Digital, everything comes out as Dolby Digital 5.1 including stereo content. Stereo content is output to the left and right front channels, but since the AVR sees it as DD 5.1, I can't use Pro Logic II or other options to process it for surround.
Ideally Apple will update the Apple TV so that we have the option to output DD and DD+ as bitstream and stereo content as 2.0 PCM.
However, there might be a couple of reasons why Apple is decoding the bitstream internally and outputting surround as PCM:
The Apple TV can now do Dynamic Range Reduction (They call it "Reduce Loud Noises"). If the Apple TV outputs the direct bitstream they would not be able to do this and it would be up to the AVR to handle this feature (called "Late Night Mode" on my Onkyo).
Dolby has a real time encoding process called Dolby Live. This is used on all gaming consoles and it allows the multi-channel audio, which changes dynamically during gameplay unlike a movie that never changes, to be output as a Dolby Digital 5.1 bitstream. However, I don't believe that Dolby has a solution to encode Dolby Digital Plus 7.1 in real time yet. The Apple TV needs to be able to encode the audio in real time in order to add the system sounds (beeps and such when you navigate the menus).
I believe that when the new Apple TV is in Auto mode, it always decodes the bitstream, processes for "Reduce Loud Noises" if enabled, and mixes in any system sounds before outputting as 7.1 PCM or 2.0 PCM.
When the Apple TV is set to Dolby Digital mode, the Apple TV decodes the bitstream, processes for "Reduce Loud Noises" if enabled, and mixes in any system sounds before processing with Dolby Live and outputting as a Dolby Digital 5.1 bitstream.
Anyway, that's my best guess as to why the system behaves the way it does now. If that's the case, I'm happy to have an option that will allow me to forego the "Reduce Loud Noises" and system sounds if I can have the Apple TV output a bitstream.