Of course the Sirens from smith/armorer quest are not the same at all as the pirate crew.
The pirates have simply just named their pirate guild after the mythical sirens because they are all women but the ones in the armor/smith quest are actual sirens that hypnotice you i assume they are disguised as mi'qote,elezen and hyur.

Now we think the female voice that awakens our echo is Siren the primal but it could be just as well be the mother crystal.

I don't remember seen anyone w/o a shadow in Gridania story line so i assume is an Ul'dah exclusive thing as when you see the only Ascian sight in game is around Ul'ddah, people without shadows are their servants?

Now we know the 12 can't be "Knights of Round" as some have suggested and they were never actually gods to begin with (maybe?) as Ferna hinted stories are exaggerated through History as more people tell it maybe the 12 are just Eorzean legends of uncommon folk that did good deeds or bad...the question is...what they did happened before Allag? maybe the 12 were the creators of the "jobs"