I wanted to create a DVD with selectable subtitles. So when I demux with PGCDemux I get the subtitles and can remux them with the audiotracks and the new encoded video in Rejig.

You could probably demux the audio with DGMPGdec. I haven't tried it so I don't recommend it. What I describe here is the way how I did my encodings and I hope this guide helps the people who have no experience in doing encodings to get their watchable GOUT. Any suggestions for easier ways to do this encodings are most welcome here.