Each core has it’s own cfg/remap/shader preset folder where they read the overrides from. When you load SNES9X and save any override, this override is saved in the SNES9X folder.
Sure, there could be a “SNES” folder and all SNES cores could save there. But what if a core is used for more systems like Genesis Plus GX? I don’t think RetroArch can understand systems, only cores. I assume it’s much harder to make it understand systems, especially when games have multiple ports on different systems. So you would need to specify a core along with the dir. Which is the same thing again.
It could have both a core and system cfg folder but that would probably create an even bigger confusion because the cores would have to read overrides from multiple different folders.
The only way i can think of that will work is if all the multisystem cores are splitted and there isn’t a single core that can be used for more than one system. And all gameboy cores would have a color and classic version. This way there would be no reason for RetroArch to mix things up, just hard code every core to it’s specified system and you are done.
Anyway, as is, i can’t think of any scenario where the user is confused, or where any conflicts can occur. assuming the user understands the override priorities.