There are other ways of accomplishing these same feats.
For example, there exists prerequisites for certain skills in order for them to show up. Edit the abilities PathOfTheMage and add pre-requisites that you will make later. Basically grants the YouCanBeAMageAbility. Then give these new Abilties to the sovereigns you wish for them to pick from... For example Markin could very well choose PathOfTheDefender, but Warrior Makes sense. Similar to Ceresa, she doesn't have to be a Mage, she could be an administrator.
What you did was ensure that the AI gets to have 2 paths at level 4 (haven't checked that, but that is what the code suggests would happen).
Of course cusom sovereigns would have to be given these Abilities otherwise you won't be able to choose these items.
The other option is to use the Prerequisite <Type>RestrictedAbilityBonusOption</Type> This will restrict certain things if a character has the particular ability, then you wouldn't have to hassle adding abilities to the custom made sovereigns. (I just don't remember if that tag works in the level up skills or not).