Having the "What You Leave Behind" theme (DVD rip or not) available for so long is probably what led to the decision to not include it on the set.
I doubt it. There are four versions of the DS9 main titles on the new CD release, and at least three of them have been available for years on official CDs. It's surely a decision to present the cue as composed rather than the altered version used in the final edit.
I don't personally have a problem with the omission/decision, I just don't think that someone who wishes it was on there is wrong to do so.