The Allagan Empire is an extremely advanced civilization that could traverse both time and space....not to mention cloning and combining different lifeforms they had encountered.

We don't know if any of the events concerning Etherys had anything to do with the Allags and their research. The civilization could very well have had a completely independent objective, and just researching the events unfolding for their own independent purposes...

Also, the Allags designed a Proto-Alexander (The Twinning Dungeon) in a crystal tower from an alternate future timeline (8th Umbral Calamity).

That being said, I am extremely excited about Dawntrail and seeing more of the FF14 story unfold.