Actually, this IS possible, I’ve set my build up this way.
It just takes some work to make it happen…
Here is my RetroArch/System folder:
The way you do this, is create your folders and drop in your BIOS files.
Keep in mind, If we’re talking about something like dreamcast that has it’s own folder in the normal /system folder it needs to be inside the folder you are creating. For example, instead of: …/retroarch/system/Flycast/ you’d want to do …/retroarch/system/Flycast/dc/
Once you have your folders setup, you then need to go to retroarch/config and Manually edit the .cfg files for each core, so they look similar to this:
system_directory = "X:\Emulators\RetroArch\system\Flycast"
What this does is change that /system directory by creating a core-override for every core. Hopefully this is something they can implement eventually, because honestly it’s a really nice quality of life feature.