Update: After updating to BIOS 0024, I have been able to play BD movies with HD-Audio bitstreams without encountering any HDMI handshaking issues with the caveat that I do not use Hardware Acceleration under the Video options of Arcsoft TotalMedia Theatre 6. I am not sure if we need an updated Intel Graphics/Audio driver to resolve this or further debugging is going to be required by the engineering teams.
On the second issue of video artifacts/corruption/pixelation with 3D Bluray movies, my previous statement still stands that this is only overcome by not using hardware acceleration for the video decoding.
My issues can be worked around by simply not using any hardware acceleration. This negates all the advantages of the latest and greatest Intel integrated GPU technology but thankfully the CPU is able to handle all the load in software.
I feel this last BIOS is a good step in the right direction but I am hoping Intel can further identify the root causes of this. It could be that TMT6 needs an update to better support Haswell.