I agree that the commentary can completely kill the piece. The worst part is when they write disparaging remarks about something that was actually very well done.
The 'apologies' for their writing actually serve to do two things to me:
1) Ruin the story.
2) Make me think that they don't actually want concrit, they just want praise of how well they are doing - the "don't sell yourself short" reviews.
It's almost as good as review whoring at getting me to click the little red X on my browser.
Like you said though, the commentary on DVD is on a separate disk, or accessible thru a separate menu. So, for those authors that are compelled, I would recommend actually making a thread in the forums, putting the hyperlink at the top of the story with something like "Commentary on this chapter can be found here: [ url ]" and then the <hr> to separate the text. Or putting it at the bottom of the chapter is even better.