No, I don't think it arrived with Dinopolis. When we get to see an image of Dinopolis back in the Reptite Dimension, it's not shown floating over water. And if Gaea's Navel happened to be land that got warped as well, it would have a different shape, it would be more wider, not to mention located below Dinopolis/Sky Dragon Island, but it's not.
About existing before Chronopolis, I think it's not a direct saying, but more like implied with Leah and the tribe she comes from. I think it's stated somewhere about them being humans that because of their isolation in Gaea's Navel they didn't got into the whole 'affected by the Frozen Flame' deal.
Besides, even if Chronopolis were in the past map, but in fact, the guy that explains the terraforming process changing to the past map while talking about how El Nido was back then, meaning that while Chronopolis is already there, it's still pre-terraforming.
And about Another Gaea's Navel, not much. Perhaps different treasure in the chests, but nothing else that I know of.