Nice video, but it's the memory card they talk about, there is already 1 memory card / game in raine, but the save ram is in common and 64 K max.
in savedata :
*.bin : memory cards
neogeo.saveram : the famous saveram, that's the one you said contained scores, right ?
I know for sure the saveram contains the soft dips settings, and what is called "book keeping", the stats about how long the games are played and how many times, see b+c+d while booting with unibios, then book keeping. You can change the soft dips from there too, or from the dialog included in raine.
No I don't see how, graphics and sounds are separated, it would have to be a tremendous bug for that. No there is probably something which is not saved correctly somewhere.
For your sound associations you probably found a game which has yet some other sound commands, there are already quite a few found, and it's quite tedious to analyze the commands to find how it's working, so I delay this for now, but it won't create any other problem by itself, it's just about how the sound commands are interpreted, it can't create any graphic glitch.