If you treat the commas are parenthetical then your original sentence means 'It is preferred over a Sony ZX-1'.
While I don't disagree entirely with John Lawler's coreferential comment, I think that's expecting a lot of Joe Public who is much more used to using commas in the parenthetical.
Reducing the sentence, parenthetically ...
It was probably on the darker/smoother side of things, compared to, say, the Sony ZX-1, which I prefer.
Get rid of the inner parenthesis
It was probably on the darker/smoother side of things, compared to the Sony ZX-1, which I prefer.
Get rid of the inner parenthesis
It was probably on the darker/smoother side of things which I prefer.
Add in another bit of punctuation because, well, who knows, but there is a natural pause there and ...
It was probably on the darker/smoother side of things, which I prefer.
Your sentence author prefers It.
Out of interest - You know the context; so what was It, and is it preferable to the Sony ZX-1 (in terms of darker/smoother), bearing in mind that not everyone knows (or applies) the rules that John Lawler knows.
ETA:
Unlike most of these 'what did the original author really mean questions' it turns out that there is clarification from the original author.
Did he prefer the ZX-1 or It? Well I think this explains it
I prefer the M and the AK120 for preference over the ZX-1, even after the update.
You can find this at http://www.head-fi.org/t/687944/999-calyx-m-with-dxd-dsd-64gb-sd-sd-storage/2670#post_10540041
Case closed.