Yes you can do that, not sure how great I am at explaining it but I'll try, I do that with Mame and Retroarch using the Mame cores for Retroarch. Hope I explain this right. This works without having to create another list or category, all your games are in the same list.
Not sure if this is what you are looking for, but recently I realized looking at the "Controls" section in Attract Mode that you can assign a different emulator per game if you want. Go into "Controls" and use the shortcut key combination already assigned or change it to your own shortcut keys for "Edit Game", then go to your game in the list and use the shortcut for Edit game and you can add a different emulator per game that way.
What I do for Mame, while a majority of my Mame games run with regular Mame there are some that require a different version, I use Retroarch and the Mame core versions in retroarch to run those that will not work with regular Mame. Once you've edited and created a .cfg file for one game in that category if you want to use that setup for another game in the list just copy/paste the cfg file and rename the copy to the rom name of the game you want to use that .cfg to, if you are using Retroarch you can change the core it uses to use a different core also.
You don't necessarily have to use Retroarch, you could use whatever you want so long as you set the executable and args correctly. I'm on Linux and my Mame games are named "Arcade". So in the Romlist directory when I edit the 1st game it creates a Directory inside Romlist named "Arcade" and creates a .cfg file for the game I just edited. Like I said from there it's a simple matter of copy/paste and rename that file to another rom name in the list use a text editor to edit the file to what you wish to use. Or you could simply use "Edit Game" shortcut for every game also, for me it's easier to copy/paste and rename the .cfg or use a text editor to edit it.
short example of what's in the config file, I am on linux. And there are other options you can add that it will write depending on what you add in "Edit Game".
it contains this :
executable /usr/bin/retroarch
args -L /home/user/.config/retroarch/cores/mame2003_plus_libretro.so "[romfilename]"
Anyway, I hope this helps.
