"There’s actually no big secret here - the two versions do run slightly apart. By the end of the film, if you switch, you’ll see that there’s a few seconds between them. I’m not sure at exactly what point the difference creeps in, but I’m guessing there’s an optical shot or fade to black somewhere that’s longer on one version vs the other.

On BD, unlike DVD, you can have multiple angles out of mux. In other words, the angles aren’t interleaved together in the same video stream as they are in DVD, but are totally independent AV files on the disc. That also means that unlike on DVD, they don’t have to share an audio track. So when switching anglers from one version of the film to the next, the video, audio, and subtitles can all be totally separate. It also means there’s no picture quality loss with Blu-ray multiangle (when done in this way). The two versions simply sit together on the disc and when the viewer uses the Angle button, the player jumps into the adjacent file at the same time code.

Had the discrepancy been higher, we’d probably have been able to find where the timing differences were and possibly remove them to keep things in perfect sync. But as it is, the timing between the two is good enough that aligning the starting times and letting them run was enough."