How can I put a VP9 video stream into a QuickTime/MOV container?
For my use case, it was enough to do:

ffmpeg -i file-with-vp9-video-and-opus-audio.webm -f mp4 -vcodec copy -acodec aac_at test.mov

This is cheating, really. The output isn't actually a MOV file, but rather an mp4, which uses a similar but not identical structure. Even so, it successfully coerced the program I'm using into opening the file.
Notably, outputting an mp4 and changing the file extension does not work, so the above command is producing output that's somehow different from an actual mp4. I obviously don't understand all the intricacies of how these containers work, but it was enough for today!