I believe I've figured out what's up with the Saints Row 2 PC audio. Since they're mastered in 'CD Quality' I was playing around and found a spec called ISO-908 De-emphasis. I used SoX to apply it to the cutscenes, and the output was *much* closer to the expected console audio. Unfortunately the base files I used were from the Linux version of the PC port, so the quality is still a bit subpar overall even if it's still way better, and many files are corrupted, but it's a starting point. I'm gonna keep working on this over the weekend and see what I can accomplish. I'll post a video later if anyone's interested.
EDIT: Some more explanation. The reason I brought up CD mastering is that some CDs up-EQ'd the treble (pre-emphasis) to try and compensate for the 44.1kHz quality and add some extra resolution. A lot of audio players are designed to recognize this and down-EQ the output back to the expected level, but it appears the audio player used by Saints Row 2 does not. It may be better for the overall sound quality to try and implement the spec in the player than to convert all of the audio, but since I don't believe I can do the former I'll focus on the latter.
This information may also be useful to the port team, assuming they haven't yet figured out what's wrong with the audio and assuming that's even still happening.