On the weekend I'm going to take a crack at this.
I think the easiest way to do this is simply take the layout, copy the folder and mll file, then rename to match the emulator.
If I'm not mistaken I could take the layout (named TEST for example) and copy the folder + mll, changing the name of the folder + mll to match my installed emulators. So the same folder, same mll, exact same contents then name it as needed. Essentially renaming it as needed for Nintendo, SNES, N64, etc etc etc.
I would however have to go into the layout editor and select the default marquee for each layout. That really isn't much more time consuming than setting up the emulator settings in the MaLa set up.