It will have instant changes, once you adjust settings you'll see the effects in next turn.
I think you make yet another good point that could translate into Tower of Destiny, in terms of rewards.
Many games give lousy rewards even after a challenging fight. You enter a really big fight, not necessarily against the main boss, and you consume all your special skills, mana, nearly all your HP, and finally win a very tough battle. Then you are rewarded for a long and hard-fought victory with a +5% water elemental amulet.
Oh, Great! For all my efforts and practically depleting all my assets I receive such small compensation. Now, my next fight will give me 5% vs. 0% (on a 100% scale) against water damage. Big deal!
Now suppose I had received a 50% water elemental amulet I would be more happy because my hard efforts were justified by a great reward. Plus, that amulet's effect I will see its impact in helping me in the next fight. I won't see any benefit from the 5% one until many fights later down the line.
I think most gamers like to see some kind of instant effect (gratification) when they receive something, especilally when they worked hard to achieve it. Obviously, you don't want the reward to be too great but something that will be useful in the next few fights, not something that will be useful much later in the game. What's the point of equipping it if it can't help you now?