Okay, I think I see what it is.
The races.txt is where the multi-class allowances are kept.
For each race, you need to add -
AllowedMultiClass =
You are right about the NPC editor - you don't have to follow the rules. 
You can do things like create a race, then not allow any classes to use it (in your text files) so that it is not available to the player and then create an NPC of whatever class and give it that race. 
Be careful if you try this trick to give a special class to NPCs, it doesn't work quite as well -> the NPC can be the special class, but depending on where it is listed in your classes file, the NPC may not be able to have any classes... 