I believed you. 7.1 layout should be fixed in the latest development version posted a few days ago, can you check? Remember that with this version you need to select audio to fixed 44.1kHz to avoid sound stutter and I'm looking for a fix to that.
Here's the results of my test with the developement build.
LibreELEC-S905.aarch64-7.0-devel-20160915211230-r23341-gb83596f.img.gz
"HD Audio passthrough no longer work and is not in the option menu anymore" still.
(Was OK on build 6 but no PCM etc.)
Config 7.1 - PCM - 44.1Khz - fixed
7.1 file: Now OK
Tested file: "7.1auditionOutLeader_v2_rtb.mp4"
All 7 channels were heard on the expected ones.
5.1 files: Back surrounds reverted
tested files: "ChID-BLITS-EBU-Narration.mp4" and "ChID-BLITS-EBU-Narration441AOT2.mp4"
Surrounds channels are heard in the rear surround speakers and nothing is heard in the surrounds speakers.
All tested files were also tested on LibreELEC on Pi3 connected to the same receiver.
The Pi3 properly rendered the channel signals to the ones they were meant to be sent.