With Warner, their DD tracks on BD are identical to their DD+ tracks on HD DVD. The problem with that studio is the inclusion of lossless audio (or lack thereof) on some titles that got it on HD DVD, but Warner seems to have stopped downgrading the audio for Blu-ray.
Paramount on the other hand downgrades every single Blu-ray Disc in the audio department, as you said. This is at least partly due to the fact that it is not mandatory for Blu-ray players to decode Dolby Digital-Plus, and so far none of them do. However, there is nothing stopping them from including a PCM track or something along those lines on most releases since each of their encodes is tailored specifically to Blu-ray spec, so there ought to be room for it as long as the video isn't already bit-starved (especially if a 50GB disc is used, as is often the case).
So, Paramount could have done many things with the audio; such as adding higher-quality audio tracks that Blu-ray is compatible with, or using only the standard Dolby Digital codec at 640kpbs, which subjectively sounds decent compared to the higher-bitrate DD+, if a little worse. Paramount could easily fit in a superior uncompressed audio track on a large number of their Blu-ray discs without paying any additional fees, but for one reason or another they choose not to. (It would be unwise to include
just an uncompressed surround track like we saw with The Sopranos, since those without HDMI or 5.1 analog would only get stereo sound.)
That's as far as I can tell, anyway. If I'm mistaken, please chime in.
edit: I noticed a flaw in my own argument in the third paragraph, I have altered it.
