I find it weird to think that EoD could possibly be in HD--for the simple reason that it's almost guaranteed it was not filmed in HD. The interviews were conducted in late 2003 I believe, and at that time there was really no HD cameras, and HD editing was pretty much unheard of. High definition original content simply didn't exist, it was only IMAX documentaries and the like, not a documentary for a bonus disc and A&E. It wasn't really until around 2005 that HD started catching on for original documentary and feature work. So the EOD master is almost certainly in stardard def.

As to some of the footage--maybe it is new scans from a print or something. After all, they scanned all the raw dailies--and the quality of the dailies clips and the finished film clips is about the same. Maybe they had Lucasfilm scan some original clips from the film to use as well. Whatever the case, the footage isn't very good, looks like the quality of a Laserdisc to me, which is why some people guessed that this is where it came from.