The default "es_systems.cfg" defines PLATFORMID 36 ("Sega Mega Drive") for the "Sega Mega Drive / Genesis" system-entry.
Would it be possible to assign an additional PLATFORMID for that system (18 = Sega Genesis)?
DESCNAME=Sega Mega Drive / Genesis
NAME=megadrive
PATH=/home/pi/RetroPie/roms/megadrive
EXTENSION=.smd .SMD .md .MD .bin .BIN .zip .ZIP .gz .GZ .bz2 .BZ2
COMMAND=dgen -f %ROM%
PLATFORMID=36,18
... and maybe adjust ES_scraper accordingly?!
That could possibly help to find better results.