No, we haven't. The fight in the Aery was against an effective cripple (only at 1/2 power and not even using his own power, while having said power turned against him). The Final Steps of Faith will have Nidhogg at his full power with no way to inhibit him, is an 8-man Trial, and he does cause some significant structural damage to the Steps of Faith based on what I saw in the Live Letter. I'm not inclined to believe he possesses calamitous power even at that level, but this will not be the relative joke of a fight we had with him in the Aery.
As for the moogles, recorded history only goes back about 1,500 years. 2,000 if you want to say we have some material from the tail end of the 5th Astral Era. There's also some history that can be gleaned from Allagan tomestones and tech, if you have the know-how to do so. Regardless, I think I remember somewhere that the first Umbral Calamity occured 10,000 years ago... which is not enough time to cause that significant a genetic shift as to create entirely separate species. A different pom-pom color (which is exactly what we got) is about what I'd expect. (And maybe for the Mists moogles to speak in a different accent, but hey...)