see, I thought the GG and master versions did use the same OS and files, but I asked on the master system subreddit and found someone who had a stock SMS and a FM unit installed and it DID disable FM sound correctly on reset. They said they never saw the results I (and now GreatFunky) have both seen - that the FM isn't disabled right. So I assumed that the GG version of the OS left that bit out.
I've been continuing to read up on this stuff a lot more and I might have a guess, but I'm really no expert.
So the audio control port, $F2, seems to react differently based on what system it is on. For instance on a stock Japanese SMS that comes standard with FM, writing 02 seems to disable ALL sound on the system, while many other systems with the FM hardware added instead reacts differently. A mark III with FM for instance disables FM but plays PSG when you write 02 to that port, while a European SMS with the added FM board will continue to play both FM and PSG sound.
I suspect returning to the menu writes 02, which disables all sound on some system, half the sound on others, and none of the sound on some. or something like that. Not sure if a different value would disable the sound properly or not, it might just be a side effect of how these boards interact together.