I have rewatched several of the more interesting sound activity scenes in both bitstream and PCM modes and and the compression/limiting issues remain the same. Double checked for any dynamic range settings might be engaged on my system and none were.
The clipping I hear is what I consider 'soft clipping' which is baked into the mix due to the combination of usage of compression and limiting. Which is something I believe many may not notice or find as objectionable as I do. Once you do notice it really is annoying.
Some examples with vocals is that it can extenuate certain frequencies and cause a raspy quality or harshness.
From my friend's wave form analysis the track is mastered at just barely shying away from actual hard limiting. I believe they said the center channel is -1.4dB from 0dBFS.
Good audio engineering practice keeps the maximum transient peaks about -3dB from 0dBFS. This is suppose to help avoid clipping in the playback chain.
In respect to bass, it is a mixed bag. Much of it is good and a few bits that are impressive and closer to ST09 mix.
Such as at the 5:50 mark when the volcano is acting up or right at Chapter 9 when the USS Vengeance warps in, those bits actually sound and feel to be hitting the lower range.
Now there are various instances in which bass may have had mixed some lower frequencies but were perhaps filtered. Whereas other bits seemed purposely mixed to be louder and more punchy.
In this regards I can understand why most feel the bass overall is fine.
I think a fair comparison between the two films is the jumping to warp sound effects of the Enterprise. They are a bit different in each respective film but similar enough that best illustrates the differences in dynamics and bass extension.
Comparatively with some recent releases. I found The Hobbit to be lacking more in the bass department than STID does. Dynamics are better than TDKR, as well in respects to bass, and not nearly as harsh and fatiguing.
I find Oblivion is be more engaging and better balanced in regards to dynamics, lack of obvious limiting especially in the vocals, and more impressive deeper bass.
The discrepancies in evaluations lie more with what people are more sensitive to or are aware of, rather than a case of possible defective discs.
Politics is like a corral, no matter where you are you'll always be shoveling it.