I'd fix the code but not sure what needs to be done, talk of alterntive groups, checking first audio? etc. I can see no options for that in ffmpeg or atomicparsley that I use at back-end to do the donkey-work.
So If anyone knows at a code level what needs to be done, or if Apple are intending fixing this nonsense, plese let me know, until then....
You can actually enable/disable audio tracks, as well as set the alternate fallback audio in Quicktime, but it's cumbersome and time-consuming. You test it out with a movie file or two to see if it makes any difference.
I wonder if MP4Tools (cli) can enable/disable audio tracks.
You also might find the following two sites to be interesting and/or helpful.
This detailed article from someone on the Quicktime engineering team seems to have some code on how to set these various options.
Here is a technical Apple Developer Library article on Quicktime Modifier Tracks and Alternate Tracks. Maybe there is something useful in there.