The line of thought goes like this (wow, everything looks nice on this university LCD).
Originally, El Nido was nothing but ocean. The El Nido Archipelago is purely
artificial, created by FATE. It was a remodeling plane that took place 10000 years ago.
A plan to include island, blessed with nature, in the sea of El Nido. The main island of
El Nido, Earth Dragon Isle, Water Dragon Isle, Black Dragon Isle... The development of
Elements, using the energy of the natural world... The distortion of memory terminal
devices called the Records of Fate that could survey and guide people's lives... The
research center staff, who had their memories erased, left the center, and began a life
outside amidst nature. This is how FATE's paradise came into existence.
This states that Chronopolis originated the Elements. Now, with that statement in mind, also consider that El Nido was terraformed and created by Chronopolis, and that this fact includes Power Spots. This, in conjunction with Chronopolis's dividing up the Dragon God into six beings, suggests that the entire Elements system was entirely concocted by Chronopolis. The instance of the term "Chrono Cross" being directly present in Dragonian Lore also suggests that Belthasar and Chronopolis were responsible for these prophecies, and thus exercised control over the Elements.
There's my evidence. The quote about the Reptite Dimension does not reference individual Elements, and neither are they tied with the collective "Dragon God" elsewhere. It thus might be simpler to say it was a complete machine, divided up to represent the Elements of Chronopolis's creation; GrayLensman's piece about the Chrono Cross being all the Elements in unison and thus a heark back to the original Dragon God machine also neatly ties it up.
Lastly, all of this raises the question about Dragonian history. Considering the magnitude and power of the fighters of Chronopolis and Terra Tower, the war was probably very brief. Dragonians that survived (probably memory-wiped, so they could co-exist) seem to have settled El Nido with the brainwashed humans in peace, perhaps scribing of the Polis War (e.g. lore about the sealing up of the Frozen Flame). Utilizing their own skills and knowledge, and given controlling actions and directives through the Records of Fate, they generated Elements and built holy spots around El Nido. I'm not quite sure when they were made extinct, due to the common wackiness of Chrono series succession. Direa states that the Dragon Tear was given to the Guldove shamans long ago, and was passed through successive titleholders. Under the Guardia XXIII/Toma XIII system, "successive" could be an appropriate term for a hundred years time, allowing the extinction to occur with the onset of the mainlanders from Porre in 920 A.D. The words of the demihumans seem to confirm this, but the fact that Dragonian ruins and inscriptions are said to have eroded away as if they were ancient constructions leans toward an older extinction. Then again, some humans and demihumans still revel in Dragonian-rooted celebrations.
