I agree the level 4 spells are just there for gameplay reasons. Kind of a pat on the back for the player having gotten that far into the game. there are some things that occur for storyline reasons and some things that occur for gameplay reasons. In Suikoden 4, the hero uses the Rune of Punishment to wipe out ships and avert an explosion, but in combat, the player uses it to summon magical swords and a weird mutilated angel that heals his friends. I think it might be more interesting to discuss what other abilities the runes have outside of combat.
And if you're talking about the Rune of Night, well, it's a rune that has incarnated as a living sword that can send people back in time and grow itself to an immense size and attack people with lightning bolts, who knows what else it's capable of? (Apparently Zerase knows, because she wishes she had it during her confrontation with the twilight rune!)