Continued thanks, Lexvo.
I do have Dolby Digital turned on with my Apple TV (thanks for the pointer).
I have finally managed to get a "video" file containing my audio to play over AirPlay in 5.1. It was a total pain: had to create a .AC3 5.1 file using Audacity, and then re-mux it into the video file that contained an empty video track and a .AAC file. [If I were converting a video file that already had a .ac3 track, then presumably Handbrake would have made this simple as you pointed out]
This technically works, though since the result is a video file it's not exactly usable for an album's worth of music (perhaps I could may Playlists containing all the videos in an album, but it just gets more and more painful).
So these tips will certainly help when I want to convert MOVIES such that I get 5.1 audio (as you note, the trick is to have two audio channels, the first being AAC (whether stereo or Dolby Pro Logic II) and the second being 5.1 channel AC3.
I still haven't found any *audio* format that I can create and which iTunes will import, such that it plays back over AirPlay in 5.1 surround.
[There are audio formats that'll hold 5.1, but I can't get iTunes to import them, or I can import them but iTunes will only stream them in stereo]