Bit of progress on the actual editing: I’ve been able to solve the couple of issues I had with the full production pipeline, so I can now use lossless video and have access to the full audio tracks for more flexible editing.

For those in the know, who might be able to suggest something more elegant:

I run the raw .mkv file through handbrake video converter, with lossy video (to make it convert quicker) but quality audio (AAC codec, 640 bitrate, 5.1 mixdown), which gives me an .m4v file with low quality video at variable framerate (unwanted) but the right audio channels. I can’t use handbrake for video because it won’t output at constant framerate.
I load this into my Vegas 17.0 project, starting with 5.1 surround settings (so it imports correctly) but then changing it down to stereo bus mode (so it exports correctly).
I run the raw .mkv file through tsMuxeR, now exporting only the lossless video file .264 with the original constant framerate.
I load this into the project, delete the original lossy video track and couple of empty audio tracks, and change the project to the correct 23.976fps format.

That gives me lossless video at the original framerate and 5.1 channel audio to play with, and rendering it keeps everything in sync.

If there’s a better way though, please let me know.