At least the PAL 2004 RC2 DVD was newly encoded for this 2006 release. The videotrack of the 2006 PAL SE DVD is not the same size as the 2004 PAL SE DVD. The videotracks have the same length but not the same size. The 2006 videotrack is 13 MB smaller than the 2004 videotrack. That's not due to copyright-screens or trailers because I have extracted just the main movie.
If you are comparing the two videotracks with virtualdubmod, you can make out really fine compression differences. Most of the frames look exactly like each other, but from time to time you can make out some differences due to encoding. So, there has to be some sort of new encoding. But don't count that you can make out some quality differences, it's only interesting that they redid the video-encoding and dvd-authoring.
The disc-cover is also redone slightly.