The free DVDAuthorGUI includes a small command line program called mplex.exe. As far as I can tell, this is used to multiplex video and audio streams into an MPG program stream before the disc is authored. The MPG file is only temporary, and is deleted on completion of the authoring.
Apparently mplex comes from the MJPEG tools project, however I can't find much guidance on how to actually use it and what command line switches it takes.
However, you might be able to do it like this: start DVDAuthorGUI, select your MPEG video and AC3 audio, add your second AC3 track, start the authoring. If you can stop the process after the muxing stage, you might be able to retrieve the muxed MPG file.