Thanks, Ady, I know about the PAL version of Jedi being better but I'm actually using the shot from DJ's project Blu and I'm not sure but I think he did use the PAL GOUT for that one. But even if he didn't, I did use the PAL GOUT in my ROTJ Reconstruction for that shot and it looks pretty much the same.
As to that change, I'm pretty sure it's just because of the crushed blacks. You can still see the neck in the SE but only vaguely (not really in the YOUTUBE video, becuase of the compression but you can see it in the HQ file.)
Also, here is an HQ video of the smoke scene, so you guys can see what I mean. It shows the shot with the GOUT element added without the smoke, then with the smoke and then side by side: