I was referring specifically to what you wanted: change configs to be fullscreen.
There are injection methods for: GB/GBC, NES, GBA, GG, MD/GEN...
I think SNES is not available... (blargSNES only (AFAIK), but that doesn't count in this case)
And GBA uses the internal hardware of the 3DS, so it works pretty much like the original GBA, instead of emulation.
But none of them can you edit configs of the emulator to run "fullscreen" or other options editable...
There's always the "Start+Select" at boot up method to make them run with console borders or original pixel size in GB/GBC/GBA games, GG games that can be defined in the options of the emulator.. Other than that...