Well, BAM is able to run different executables, I don't know since which version though. Here's my modification to the fplaunch.ahk (1.295 wip 10) to make this happen : 
At lines 562 & 564 I replaced the following :  
"%emupath%\%executable%" 
with : 
%emupath%BAM\FPLoaderNew.exe /FPEXE:"%executable%" 
After this, just specify which other than the default settings.ini exe you want to run in the settings/fpexetables.txt (tablename[enter]fpexe.exe[enter]...)