I am not sure why but I find all of this nitpicking entertaining, and I am happy to be a part of it. In my opinion, the best thing to do is to make it look as good as possible without changing what was originally intended. In other words, if there are color channel misalignments on the original negative, fix them. If there are scratches or burn marks, fix them. If there are matte lines, fix them. Fix any artifacts that are as a result of putting the movie together and something going screwy. Just don’t add, change or remove scenes like the SE’s did.
Fixing channel misalignments, yes. Scratches and burn marks, yes. Matte lines, hell no.
Everything on the original negative, keep. Anything that happened as a result of duping the negative or creating various prints, fix.