Just to add some details about my LE11 vs LE12 comparison: I did quite a bit of low-level checking while actually playing the passthrough stream. I compared the relevant /proc and /sys entries, ALSA/device state and the kernel-side flags/parameters between LE11 and LE12. I also checked the state while the stream was actively playing.
I couldn't find any meaningful difference there: the same HDMI device is exposed, the relevant capabilities/flags look the same, and the kernel-side state during playback looks essentially identical.
The important part is that this is the exact same TX6, TV and HDMI connection: LE11 passes the bitstream correctly, while LE12 does not — the TV only detects LPCM and passthrough results in digital noise.
So I agree that Kodi audio handling is worth investigating. My tests just make it look less likely that there is a simple difference in the underlying HDMI/driver state between LE11 and LE12. Of course, there could still be a difference in the actual data/API interaction that isn't visible in /proc or /sys.