RTF is a global modification that replaces all towns in the game.

In general, due to the effect of commander skills, it won't be possible to properly divide magic into elements.

I'm not sure if it's a good idea, but have you considered moving the commander skills to "Spellcasting" and/or "Education"? Of course, then you'll have to come up with something to replace the skills in the schools themselves, but you could implement a reverse transfer with possible enhancements.