I didn’t notice any problems with the subs from Project Threepio, but I demuxed with eac3to and remuxed to MKV. The playlist that I selected was the one with the '77 crawl.
EDIT: By the way, I checked the demuxed video against Despec 2.7, and they’re in sync right through to the end, so there doesn’t appear to be a GOUT-sync issue. Perhaps the seamless branching has something to do with it.