I got this release on Saturday as well. Here are some things that I noticed. (I'll try to update with better/more screenshots later).
The opening credits and title card are from the Japanese version, rather than the previous Kraken releases which were Toho's International versions (which were the International versions that Sony remade for Toho).

The Japanese version has burned-in Japanese subtitles, and the English subtitles are merely placed directly on top of the Japanese ones. It makes things rather difficult to read.

The subtitles are literally all over the screen. They appear over signs (like on the boat in the beginning). The font will change to match what they're naming. In the beginning, when the main character (I suck with remembering their names, sorry) discovers the drifting boat, the song he's listen to on the radio is subtitled. Interestingly, there are two sets of simultaneous subtitles. One with the English translated lyrics, and another with the romanji. Subtitles also change color (white and yellow), based on if a character is speaking vs a voice from off-screen, like a radio announcer. Someone else on a Facebook group pointed out that this is common for anime releases, included Section23's (Kraken's parent company) other releases.
As for picture quality, I don't have the Toho blu-ray, so I can't compare directly to it. But, knowing that the Kraken release is using a Toho transfer, it does look a bit soft (but not that bad), and the color looks a bit muted. I don't see any print damage though, and the image seems pretty stable (I compared the BD to my G85 LaserDisc, which was shaky as hell).
For the Language tracks, I have a feeling that they music and effects are the same between the English and Japanese language tracks, and that they just swap out the languages for the two tracks. Both tracks are DTS-HD 5.1. I noticed this when I changed languages while the movie was playing, and the music in the background (there was no dialog at that moment) sounded the exact same, no change in quality. I actually had to double check that the audio track had actually changed. This is probably why the scream is missing, since they're only using the dialog from the International dub, and not any of the dub's music or background effects.