Correct. For HB 0.9.2 eddyg did a bang up job of figuring out how apple was putting the ac3 passthru into an mp4 *immediately* after AppleTV Take2 was released. He worked for two days straight reverse engineering the Intro movie in the take 2 image which uses the exact same scheme as their HD movies. Including the appropriate atom. 0.9.2 was delayed just so we could get this in.That aside, I am stoked that I get the unaltered AC-3 AND a PL2 file. SO that means the bit rate selection (160 max) is just for the 2chnl.
Once he had that done for libhb and the cli. We desperately wanted to get it out so in the macgui, I had to work with most of the interface we already had, which has always used the "Codecs" dropdown to couple the video codec with the audio codec (ie. h.264 / aac) . The other issue is the the macgui has always only provided for two audio tracks in the interface. We would now be using them both up. The solution I went with was to basically cheat and make a modified h.264 / aac codec setting called h.264 / aac +ac3 that tells hb to set the audio the same as before for the aac track, but to slip the unaltered ac3 passthru track of the same source track you choose for aac into the encode. So it is pretty much automatic however its not totally transparent to the user. This method also left the second track in the macgui open so a user could choose another language for track two (which in this case becomes track 3 in the final encode) .
Having said all of that, don't get too comfortable with this shortcut. HB no longer contains the Codecs popup in our svn and you can mix and match up to four different audio tracks in an encode. AC3 is no longer "slipped in behind your back" either, its chosen just like any other track. It also shows the bitrate and samplerate used right in the window so you can see it is using the input track bitrate for the output (of course, since its pass thru you cannot modify it with ac3).
Hope that helps clear that up as far as handbrake goes.