That dupe neg talk was just speculation on Robert A Harris’ part. I’m pretty sure we know for a fact that George had the changes cut directly into the o-neg. RAH is correct, though, that the o-neg is not needed for an amazing OOT restoration.
Now that it’s Disney’s money to spend on such a project and not GL’s, I’d say the chances are much greater. George even changed his tune from “my original vision” to “it’s too expensive right now” not long before selling the company. I honestly don’t think it would bother him if the remastered original were packaged with a remastered SE.