OK, official word from Japan is that there is no difference between using the 5.1-channel outputs whether you're configured for "2-ch+5.1-ch" analog out or "7.1-ch" analog out with the rear channels turned off. Both of these come from decoding the lossless tracks (usual caveats apply: Secondary Audio must be OFF or if ON, then there can be no menu clicks or Secondary Audio in the stream).
The reason for those shaded areas in the manual is that the only way you'll hear exactly what was laid down in the studio is if you use the 7.1-channel out and use a 7.1-channel speaker system (in other words, you'll get the original, full 7.1-channel mix from 7.1-channel original soundtracks). Mixing a 7.1-channel mix to 5.1-channels can still technically be called "lossless" (since you're losing nothing to compression) though you are (in a sense) losing some spaciousness from the original 7.1-channel mix by mixing down the rear and side channels.
And yes, I know about the meta data in the lossless mixes that can actually allow a single lossless stream to carry both 5.1 and 7.1-channel mixes, both designed by the product/mixer/engineer and optimized for each configuration. But that isn't possible in PCM 7.1 soundtracks (for example) because there *IS* no meta data to describe alternate mixes in a PCM stream.
So for those of you using the 2-ch+5.1-ch option (so you can send 2 channel sound to your TV and 5.1 to your receiver), fear not as you are getting lossless audio decoding.
Perhaps more interesting is what can happen when you leave HDMI Audio ON when using the multi-channel analog output, and that will have its own post since it is a new topic (but not here, as the moderators took the link out of my SIG)...
-CB
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Chris Boylan
Home Theater Editor
www.bigpicturebigsound.com