Does anyone actually owning the set know if 1) the pilot is included and 2) is the original music from the televised programmes used (which would mean that the DVD producers have solved the apparent copyright issues) or is it the re-dubbed alternative DVD score as per on the original DVD release?
I own this set by now (blu ray). There are seven additional featurettes added to the second season which are not part of the single season edition. This would account for the third disc. The pilot is not included.
I can't comment on the music, as I have not seen this series on TV.
As far as I know, the extras are the same for the DVD boxset. First, both sets have 5 discs. Second, it says on the cover of the blu ray boxset that extras are in standard definition only, suggesting they were simply taken from the DVD-edition.
But two be perfectly sure, I'd suggest to check the "2 entertain" website or some reviews (e.g. from the imdb).