You can be synced down on SMN, but the traits you unlock to change emerald and topaz carbies into Garuda and Titan are still in effect. While they do get new moves over the carbuncles at high enough levels, beyond that they're just skins to the best of my knowledge. For Ifrit, it's possible the actual Summon III skill has a much lower level requirement than what you need to flag the quest(which could well be simply because that's the level you need to be to do the storyline fight).