singhcr said:

How do you encode a matrixed 2.0 PCM audio track, exactly? I have the PCM stereo file from Jonno but I need to author it with the surround flags.

don't touch it. the audio is already properly flagged. just add the pcm to your project. if you're going for a simple remux with tsmuxer, run the pcm through eac3to and export as .w64 or tsmuxer wont recognize the audio file. don't worry, you're not re-encoding. you just change the container. if you use mkv, then this step is not needed.