I'm not entirely sure where I should post this theory, but here goes. Upon rewatching the opening CS of XIV, we saw that Midgardsormr was attacking the empire and laid to rest in Moh Dhona releasing all of the primals. This was the birth of the primals which set out to take new refuge onto the land. Bahamut was the only one who was not summoned because he was already imprisoned in Dalamud, thus meaning he is not a primal. Nael knew that Dalamud was more than a lesser moon as he referred to all primals as "False gods." I have a strange belief that Nael knew that Dalamud was actually the prison of Bahamut and felt that Bahamut was the one true god to cleanse the impurities of the land.

Just my theory.