Hmm, I don't think it's so cut and dry. In comparison.mp3, some scenes are better in the first version, some scenes are better in the second version... All of the second versions of the scenes have a TON of clipping, much more than the first versions, but that could just be an artifact of the conversion from AC3 to MP3. The "I find your lack of faith disturbing" scene stands out as being enormously better in the first version to the point where the second version is so muffled and lacking in treble that it sounds broken...

Assuming that the terrible clipping isn't inherent to the soundtrack itself, I think the second version is better in the larger number of cases, except for that one scene I mentioned.