Those are his lords, so he has to choose whether to enable them in Custom Battle or not as I have to cater to various other mods as well and can't just reserve all of Custom Battle for him, especially as it would then fill up my already limited list with factions that hardly anyone would use if his mod is not in use.

I don't know how you are getting on the idea that this would affect campaign in any way, all factions are unlocked so all of his custom content should work just fine.