How 'bout a quest rule simply called "Wand Fire Fix"?
If you place burn or wand fire flags and then you play your quest, you'll notice that when you fire the magic wand at these flags, the magic goes right past these flags, so they can't be triggered, unless they happen to be on the edge of the screen, the only place where wand fire seems to appear. Even when the magic hits a 'magic sponge' combo, it does not turn into fire when you have the magic book.
Perhaps there could be two quest rules:
+The first makes it so that wand magic will turn into fire if it hits wand fire or burn flags.
+The second makes it so that wand magic turns into fire when it hits enemies (besides enemies that are immune to magic, such as darknuts); this only happens when you have the magic book of course.