My Sega FILM muxer now successfully roundtrips! I can take an existing Sega FILM file, extract the streams and remux it using my muxer; the game plays it back perfectly.
It’s happy to accept different spec audio, too. For example, I replaced a mono 16000Hz stream with mono 37800Hz, and the original game’s player was fine with it!
The only thing that I currently haven’t gotten working is using FFmpeg’s Cinepak decoder to author new media - but that’s not my muxer’s fault. Think I’m going to submit my muxer now, then look at what I can do to get FFmpeg’s Cinepak encoder to play nice.