The original negative already has the effects composited - yes, the removal of the matte-lines would be a byproduct of recompositing, which would destroy the integrity of the effects. If someone would find the link to that article I always quote to back up that the compositing is an important part of the original effects, I'd apprecite it (I'm on my phone).
And all those shots in my previous post have clear matte-lines - look closely at the edges of the ships, they all have thin darker lines around them. And remember, that in those examples, the originals are from GOUT, which accounts for much of what you may call "faded" look.