I've begun looking at various transfers to see what else has been done on the film...
The whole flight sequence which ends on the matte painting of The Raven in Nepal was also screwed around with for the 2003 DVD version. (restored on the Blu-ray)
Top: BD Below: DVD
Besides removal of matte lines, the shape of the miniature was tweaked when seen on the plate in front of the Golden Gate bridge. The plate (the water around the plane) was also affected in the process. (I'm not entirely sure in which way this sequence was altered, as it doesn't look like just a regular recomp, the result is ugly) EDIT: It's just a recomp, but the element has a slightly different shape.
Removal of matte lines and digital manipulation is visible when the plane flies behind the clouds:
The animated red line was also redone in the process - in the original I think it was animated over the map and then that was blended with the plane element. In the redone sequence it appears on top of both elements without any transparency, clearly seen in this example:
There's also a smudge visible on the matte painting above the left house in the DVD version, not present on any other transfer I've seen:
What did surprise me, is that the HD-broadcast (WOWOW) contains the original flight to Nepal sequence (despite keeping the redone clipper matte painting a few scenes earlier). However, the HD-broadcast displays clear signs of noise reduction in this particular sequence compared to the BD where some reflections in the water along with optical grain and dirt is gone.
More comparisons of other changes are coming if there's interest.