@thatgammon - I know this is an old question, but better late than never?
If understand you correctly, you want to use the Other Emu Config in Mala to launch a batch file and have Mala pass the rom name to the batch file so you can use an "if %1" statement to perform some logic based upon the rom name.
I just ran a quick test, and it appears Mala can do this with no problem. Its working for me, so feel free to respond and we can troubleshoot why its not working for you.