It gets completely insane if you think about what "negative" really means in the context of the most complex FX scenes that were originally assembled with ILM's old optical printer. A space battle scene would have a background plate negative, then there are negatives for each effects element, and all their mattes. If you digitize each element's negative separately, you then have to reassemble all the layers of the scene and match the original registration and color correction of each element. They did NOT do this, or there would be no matte boxes anywhere in the DVD, and there are. Truly rebuilding the film digitally from scratch (in a way that preserved all the original photography) would be a staggeringly monumental undertaking.
Because everyone's saying the SE scenes look better blended with the original film now, it might sound like they did it the hard way, but on the other hand they've talked about not having enough time so that would suggest doing it the faster way. The faster way would be restoring the SEs rather than the O-OT. They may have used a combination of techniques, though. For FX scenes that aren't as complex as, say, ROTJ's space battle, they may have gone back to the O-OT for the negative and then recomposited the FX on top. And clearly, the O-OT was completely digitized at some point, if not for the DVD then for the SE.
I think I read that the bonus materials were made simultaneously with Lowry's work to meet the DVD release date, which means the bonus materials are NOT made form Lowry's restoration because it wasn't available yet. So you're probably looking at the O-OT footage as it was remastered for making the 1997 SE. That wouldn't explain the pre-Ep. IV opening crawl's restoration but maybe they just had that done separately for the DVD.
It would be interesting if someone in the know would dissect it all in an article sometime.