I just made an account only to answer this since I was struggling with something similar: all my games were in .zip format (around 2000 titles) and didn't want to unzip everything, so I wanted to force retroarch to play specifically the right core for each platform (gb, nes and snes), in the "associated platforms" page for retroarch you can select each platform and force command line commands.
For example, you can specify -L "cores\nestopia_libretro.dll" for nes titles and -L "cores\snes9x_libretro.dll" for snes without the need to create "different emulators" just for a specific platform
