You bring up some very good points. Since I haven't done film editing, it is very helpful to hear what kinds of problems arise and how they are currently being fixed. Thanks!
One step of MPEG-2 encoding (and I guess JPEG as well?) is a DCT, which results in frequency information (and some of that information thrown away, for the compression). What I'd like to try when I get there, is to manipulate that frequency information and see how it affects the image. If I can cause a color change, then we might be in business. If that doesn't work (and of course, it's pretty unlikely to work) I see two options: 1) Match the OUT scenes to the SE (results in less re-encoding, since the OUT scenes will have to be re-encoded anyways), 2) Re-encode afterwards, as you say. I'm also hoping that I can pull off the idea of a partial frame re-encode. I'm still decoding program headers at this point, so I'm pretty far off from decoding frames.
I also wonder if the end result will be better than the OUT disc. But, "I have to try". If none of the MPEG tricks end up working, at least everyone can choose the patches they want, which I hope is a welcome benefit.