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

no hooks... it seems the effect of the skills is completely embedded in the executable file.

In that case, your option is the most suitable. Now, we need to rename some spells and change their icons, and for some, change the effects if possible. The only thing is, could you make it so that the skill granting protection is in earth magic, but it can be upgraded by having earth and air skills?