The way I saw it is they are simply divinities true, as they themselves claim to be. And do not intervene with the affairs of mankind. The lore book describe Althyk as the first to come from the 'Whorl', and along with Nymeia gave birth to sisters Menphina and Azeyma. More would come to existence through whorl like Thaliak, with some going on to 'create' additional gods of the Twelve. Iirc Nymeia just created Rhalgr on a whim as creation was getting out of control. And then there's Oschon, who just popped up out of nowhere. Not even the other gods know where he came from. It's all so mystifying, and I love that. Were they around pre-sundered Etheirys, or did they come after? I felt it would've been ok to just leave these questions alone.
I feel the direction they are going is what leaves the potential for holes to pop up all over the place. Are they sundered as well? If not, how did they avoid it. We learned that Amet, Lahabrea, and Elidibus avoiding it was no small or easy feat. How does Emet know their true identities? Unlike my above statements, these questions do indeed need to be answered, or it leaves a giant hole. It's nowhere near as mysterious as the twelve just being gods, whom for some reason have decided to make themselves present to certain members of mankind.
After a little more digesting, everything going on with Golbez, the archfiends, Azdaja (gorgeous dragon BTW) could have taken place during an intermission from the previous plot with Hydaelyn, Zodiark, and Endsinger. I know Yoshi and team wanted to move on, but it was without question very rushed. Garlemald, the 13th, and Elpis are each expansions within themselves. They could have put the story on hiatus to explore the Garlemald and Zenos, and the 13th and Golbez. Easily. They made Anima, and two archfiends dungeon bosses, and this could all have been avoided.