I dont know if you are familiar with the program Closemul.exe, but it came around like I dunno, 5 years ago as a inbetween to try and do stuff like this. Basically from your front end you would launch closemul with arguments, and it had its own ini to launch the emulator, along with features like killing emulator processes with esc key, running additional apps, mounting virtual drives before emu launch, and demounting after, etc.
You would basically put a copy of closemul.exe and its ini in every emulator directory to customize how its launched independent of front end. Then the front end calls closemul and passes the rom name.
At any rate, that may work for this, cause closemul may stay open while it launches castle crashers, then LB checks for Closemul.exe instead of castle.exe.... I dunno ill try it.
It is good to know its not all steam games though.
Again thanks for the help.