It would depend on when that scene on Marsha went missing. Is it gone completely on the 35mm elements at Fox? If so, they'll have to track down another source for picture and audio. Or did it get omitted when making the HD Master of that episode from those elements? Less complex scenario, but...
Don't forget that if they add the narration to the Pilot and the scene to Marsha that would also entail creating all the various subtitles and possibly tracking down the audio dubs for those scenes as well.
I'm not doubting it aired, but is it part of the episode's narrative? The description reads more like a specially produced commercial promo than a scene from the story of the episode.
From that link, "Cut #1" is the opening narration of the Pilot episode that has been discussed many, many times now.
"Cut #2" (from the season 2 premiere episode) doesn't sound like anything that's in the actual episode, but sounds more like a post-episode promo that simply hasn't been included...
The only missing voiceover I'm aware of is the opening in the Pilot, which has been discussed multiple times so far as having versions with and without that voiceover due to its unique production.
I would wait it out longer than a week. It may take them longer than that to track down why the issue occured on the HD master (I'm assuming it's at least to the mastering stage as it is the same issue across BD/DVD/Digital), and depending on what caused the problem, there could be weeks further...
I've never seen any scratches on a blu-ray disc ever effect playback. Fingerprints and smudges? Yes, but those are easily wiped off. Scratches? Nope. I've taken knives to the bottom of some discs and never had a problem. The hard coating works.As for being packaged with scratches on them...