For one thing, both Steena and Direa are adherents of a religion based on the Dragon Gods as separate entities, and it is therefore just as likely that their dogma states that the Dragons were always separate and controlling their colors. As for power points, it's also evident that they had to come into existence after the islands did. That means that FATE had at least something to do with their creation. Plus, if FATE is capable of terraforming on that level, it should be no problem to weaken the planet in such a way that power leaks out (assuming an FF7-esque power source with an actual geographic location), or (assuming an ethereally located power source) since it was able to use the Flame to partition the Dragons, it should be equally possible for FATE to use the Flame to concentrate and direct the planet's energy.
EDIT: It's possible that the power spots existed at the bottom of the ocean pre-terraforming, but I find it doubtful. They couldn't have existed anywhere before Dinopolis was sent back in time, as neither they nor Elements seemed to exist in CT, and they certainly would have drawn attention. They may have come into existence spontaneously when the Dragon God suddenly existed in that timeline, which is entirely possible, but would require a massive coincidence if for more than one to exist above water in the Archipelago, and they are definitely referred to in the plural (Most of the map area in CC is water, and power spots would have appeared worldwide AND would almost be fairly rare, or else it would be places lacking power that would be interesting). And after the war, which I presume to have been a pretty quick affair from the events in the game (someone correct me if I'm wrong), the islands were created and the remaining Dragonians migrated, at which point they began using power spots to create Elements, after the Dragon God had been divided by the Flame.
I just sorta realized all that just a few moments ago, so yeah, that's why it's an edit. It really is supposed to be part of the same idea, so it goes in the same post.