Dual gem mastery helps when you have a level with many (4 or more) different available gem types. Usually, when you combine different-colored gems the result is weaker than a "pure" gem. Dual gem mastery helps combat that weakness.
Fun game, I just wish you didn't have to fight enemies in spaces you've already defeated. It makes it a pain to go from one area to another (I like to fight higher level spaces before I go to a castle so i can level up my animals).