But its more like than not purely coincidence. It is possible it might be a nod to the Composer of Chrono Cross Mr. Yasunori Mitsuda, but that's just speculation on my part. As for the overlapping dragon part, I would dare say its not the first time and won't be the last that plot lines, and core plot devices overlap.
Though this does pique my interest immensely, and I shall now go do a bit of research for a possible connection.
If I'm not mistaken though, the "five huge dragons of Artago" were already part of the storyline long before Chrono Cross came out. They just now got to it in game format.
Do you know by name Adol Christin? Adol Christin...Thousands and hundreds years ago he was born at the small unknown mountain village. Where is situated in the north-east of Eulope, the western end in Eleshia continent. He was a very brave adventurer, who had traveled all over Eulope and foreign countries since at the age of 16 till the death of 65 years ago. He who was born as the poor peasant´s boy was common by acknowledged to be a curious and active youth. In particular he wants to know the outerworld. One day he met the traveler who stopped in his village, from when he began to go to his own adventurous trip. In those days -only on foot & ship- his sphere of activity was marvelous. In th south Afroka continent, in the east the Tigres of Crietta, the north pole, etc. As for as we know, his spirit of adventure to unknown strange countries is astonishing. Can tor of that he kept his adventurous diary concerning ocurrencies which he met wherever he went. His most important works "The five huge dragons in Altago", "Celceta the sea of trees", "Kefin the city of sand", etc. His works -more than a hundread ones- are preserved in the basement of his birthplace and at present they are quietly asleep in a striking contrast to his activity. When we read them, we can know his footprint. The following story is the part of start of "Ancient Ys Vanished", this story is the first memorial to be translated and novelized. The place of adventure is Esteria sleeping in the ocean floor. The story will develop as he proceeds to the land. Light and darkness, the disturbed and chaotic era. We want you to read through the same feeling everything he experienced himself.
While Ys Eternal does predate Chrono Cross by over a year, it's rather unlikely that Falcom had actually mapped out the plot of this game back when the Five Dragons of Altago first got mentioned. This isn't the Kiseki franchise after all. They made some notable retcons to Ys III when Oath came out and are definitely going to do the same to IV with Celceta. For an example of a major about-face on central plot elements, look at Mask of the Sun's portrayal of the Eldeen civilization, then look at every other Eldeen we've seen in the series. Falcom's got no problem changing their mind on things between making one game and making a later one; they may have had some vague notion of Adol's adventure in Altago but I don't believe the specifics were in mind over a decade ago. More likely it was something along the lines of 'Adol goes to an exotic locale [ruled by five dragons], stuff happens, there's at least one new love interest, Adol sails off into the sunset again'.
*Dusts off a musty old tome from the library of Vane*
Dragons have long since been traditional in RPG's as guardians and gods, although Lunar did popularize the idea quite a bit. Bahamut Lagoon is one example.The guardian gods of the land resided on sky islands that maintained the world, one such dragons was said to herald destruction if awakened.
Then there's the Breath of Fire series, IV had especially heavy reliance on the dragons as gods of nature. Fou-Lu was a dragon god himself ( or at least half of one. the other half was Ryu), the other dragons you meet along the way are other excellent examples.The dragon of winds residing high in the sky, the dragon of water asleep in a riverbed, and so on.
No matter how you slice it, dragons are always part of the most respected creatures in mythology, and as such are almost always portrayed the same in games. Many cultures do see them as a form of guardian or god, so the end result is a being of immense power, whether it is a good or evil being is up to the writer (and sometimes the reader/player) to decide. ^_^