I never quite understood how Chronopolis was equipped with the powers to terraform an entire spot of island. I've always sort of shrugged this mystery off, leaving it to the advanced technology of the time city. However, it just became clear as I was completing the Reptites entry:
In order to control the natural
energy itself, FATE divided the
one Dragon God entity up into
6 weaker plasma life-forms...
This follows an explanation that the Dragon God (whole) allowed the Dragonians to control the natural world in their own dimension.
Now, I just made the connection that in acquiring the powers of the Dragon God and its fragments, FATE was presumably able to use their elemental effects to shape El Nido. The original powers over nature became a sort of tool to Chronopolis. This seems logical; in the absence of terraforming equipment, what better to use than an advanced machine created expressly for controlling nature? What do you think?