It's been a while since I posted this question. However two things that happened that make me retake it.
First, as opposed to gonk's comment:
Multichannel PCM on Blu-ray discs was done initially because the early players didn't include decoders for the new audio formats. It is a significant disc space hog to use, and newer releases are using multichannel PCM less and less. Where nearly all releases used PCM at first, I'd guess that now fewer than 25% use it. There are even some Blu-ray releases that are only using Dolby Digital or DTS. Over the next year, I'd expect studios to move entirely to Dolby Digital Plus (which is just an advanced form of Dolby Digital, also using lossy compression), DTS-HD, or the two lossless compression options TrueHD and DTS-HD Master Audio. The latter two can offer the benefits of PCM (no lossy compression) in much less disc space.
I see that most BR titles are still released with uncompressed PCM as opposed to TrueHD. The same applies to those to be released soon. Even those that come with True HD also feature PCM.
Second, Sony has a firmware upgrade for the BD-1 that allows it to decode True HD so the discussion, on my side, is now futile
Just ordered a set of 5.1 interconnects to use uncompressed audio via the 990s analog inputs