This Allagan node confirms Miqo'te existed during the reign of the Allagan empire. On top of that, there was some loading screen trivia that was found, and one of them explicitly stated that scholars in modern day Eorzea almost unanimously agree that the Miqot'e originated from Meracydia. This is reinforced by the fact that the Sunseekers traveled across the "frozen seas" from a continent to the south. Given the empire's war with Meracydia, isn't surprising at all that they had some contact with the Miqo'te tribes living there.
Take a good look at some of their mechanical and biological creations, too. They definitely made sphinx-like machina (Such as the one found in The Aetherochemical Research Facility or on top of the flag ship), as well as anubis-esque biological entities. Seem like odd choices, don't they? Unless maybe, just maybe, they're a throw back to a day when they once worshiped the sun god, not unlike a certain ancient African culture.
Funny that, Eorzea also sort of looks like Africa.
Could it be that the Meracydian temples, the Allagans, and whatever civilization the Temple of Qarn was built by (which also has heavy egyptian-based themes and architecture) are somehow related? Oh, my. So much speculation.