Umm... No, every Slot must have a Character assigned. You can make your key maps slot-based instead of character-based but it still needs the character names to fill in any macros. If you don't have ISBoxer generate macros with your character names, you can make everything slot-based but then you're going to have to make your own follow and assist macros... so I'm not really sure what gain you're actually trying to get out of that

All I do for variations on the same team is swap characters in to my existing character set and re-launch. My mappings are class-based, using Action Target Groups and sometimes virtual mapped keys (not really necessary but helps keep the number of Actions down to cover each class/spec), so it generally doesn't matter who is in what slot. I spam my DPS key and they do their spec-specific rotations, I hit my targeted AoE key and whoever has a targeted AoE gets the ground targeting circle up for me to aim and click, etc.