When creating the DE they did have access to the reels I believe, and could therefore scan whatever they wanted to use (there are several cases of alternate shots being used). However a lot of the FX footage for the model work was lost or destroyed so no re-compositing was done.
I suspect that the 2009 DVD & Blu-Ray is a new scan, as the frame geometry is different vs the 2002 DVD and HD broadcast (I'd guess the HD broadcast was the transfer they used for the 2002 DE). Based on the trailer transfers included on the blu-ray (footage least likely to be messed with), and some of the LD captures I've seen, I'd conjecture that none of the post LD transfers reflect the theatrical presentation:
-The 2002 DVD and HDTV copies were re-color-timed according to the people who worked on it. Compared to the trailers and some LD captures it has a heavy red push and has a low gamma value for some reason, however the highlights are well preserved resulting in high contrast in several scenes with no blown highlights. The print, unfortunately, either wasn't properly cleaned or has a lot of dirt embedded in it, as it's a very dirty transfer.
-The 2009 DVD and Blu have different color timing that in some cases matches the trailers and LD captures, however in place of the red push for the prior transfer there is a heavy blu push, and the color saturation has also been increased. The gamma issue seems to be fixed in most scenes, however it seems to have completely washed out certain shots, while in others the highlights and black levels are blown out to clipping (some one wasn't watching their scopes it seems)*. And of course there are a lot of issues with unnecessary levels of grain removal, transfer errors, frozen grain fields, etc.
To make matters even more complicated, in one of the TMP documentaries there is spliced in footage of the transfer made for the blu-ray release, before it was DNRed, color timed, and went through digital dirt removal, with yet still different color timing! All of these reasons are why I'm looking for a basic digital copy of the LD that retains color fidelity, as I'm wagering it's probably the transfer that was least tampered with going from film to DI.
*The black levels can be explained because the many levels of optical compositing raised the black level of the film print, which resulted in many shots having a dark gray background for space. The colorist must have tried to "fix that" by lowering the black level of the space field so it's actually black, but this also crushed a lot of detail in several of those scenes.