I could never understand the workflow they did. 1) Scan, 2) Colour Correct, 3) integrate new FX, 3) Dirt cleanup. It's pretty much the opposite of how normally things are done as far as I understand it. First you scan. Then you clean it. Then you colour it. Then you integrate the new footage and match it to what you have.
If I was Lucas, knowing I would return to the films, I would have also saved each stage. Have a pure raw scan, just in case you need to start over; you can always re-comp the new additions back in. Have a backup of the new scan with colour correction, just in case you want to do a new cleaning pass from scratch. Why wasn't this done? HDD space is so cheap and Lucasfilm is worth so many hundreds of millions of dollars. I mean, okay, you would have to spend money on having Lowry clean it again, but with all the finicking with the baked-in scan, the difference can't be that huge, you would save time by simply returning to the source.
Unfortunately it probably comes down to the fact that Lucas himself supervised the 2004 scan (sad isn't it?), and he can't be bothered to do this for every scene of every film all over again and would rather just have them bring up the brightness levels if it looks sort-of right, at least to a not-very-discerning level. I mean, he thought the 2004 version was great after all, I gather that it is his cronies that are attempting to respond to criticisms. I read some response a few pages back by one of his employees that attempted to lay the cause on the way HD video responds to film; it was so ludicrous it made me laugh sadly and shake my head, fully out loud. Are they fucking kidding me? But probably most people reading that statement don't know any better, and buy it. But the moron saying that knows full well that he's lying to everyone's face and hoping that his audience is too stupid to realise they are being had. That's the sad reality of Lucasfilm these days.