I think there is a way to input a non-selectable character in Mugen. There has to be because Infinity's Marvel Vs. Capcom: EOH game has Symbiote Onslaught in it and they found a way to make him disabled (with the exception of going to random and trying to get him that way). Just make it so that their icon goes off of the character select screen. Of course the char will still be there but his icon will be non-existent because it does not appear. I've done this with the DCvM version of Green Lantern on Winmugen just put him at the end of the character list (the one with 60 slots) in the select def and he appeared off screen and un-selectable. Incase that does not work here is another tip (this is all guess work BTW) delete the characters icon and they may appear to be off screen, but still put them at the end of your char list and set them to be the boss/sub-boss.