Well to really be able to do that would require developing the emulator further or coding part of the emulator or hooking in to it.
The simple solution is config or command line arguments. You'd need to set it up per game outside of LB anyways, so setting it up inside of LB would be no different. It is the same logic that I use with RetroArch, except if Desmume has proper per-game command line argument handles (like screen orientation), or has custom config loading as well you can set these per game.
Edit a game, and below the box where it shows the target rom is a command line parameters box. Here is where you can set up loading custom configs or loading specific settings through the command line. This is all predicated of course on one of these options existing. If they do, the fix can be very easy.