Relationships of the Twelve

[Yrusama]

The interesting tying about gods is that they like to bend the rules on birth sometimes. If we assume that male + femal = conception of child, then we can infer that Thaliak and Azeyma were the whole parents of both, because there is no way the siblings could otherwise share a common parent.

But then there are those religions where male gods have been known to give birth and others where conception occurs without a pregnancy and the child simply comes to be.

This. We can't accomodate for a third parent shared between Llymlaen and Nophica without considering:
A.) The third parent is hermaphroditic/unisex
B.) Homosexual procreation is possible among gods, making the gods' genders moot.
C.) There is either a thirteenth god or there is a parentage line missing (another of the twelve getting involved)

It's possible that one of the sisters was born of one parent, and the other was born of both. (e.g. Llymlaen is born of Thaliak, and Nophica is born of Thaliak and Azeyma). It's also possible that both parents birthed their respective children this way (parent:child 1 to 1) and the girls are not sisters in the genetic sense.

This chart shows me something interesting: the umbral god Althyk spawned both astral and umbral children (Azeyma and Menphina), whereas the umbral Rhalgr only spawned astral children (Halone and Byregot). The builder and the fury spawn from the destructive meteor, just as we Eorzeans rebuild and fight back in the wake of Dalamud. I'm probably just overthinking it, as it's far from likely that the loremasters of the original 1.0 were actively foreshadowing the Dalamud storyline when they wrote the gods' backgrounds. Nevertheless, maybe they can use this somewhere in-game.

[Orophin]

C.) There is either a thirteenth god or there is a parentage line missing (another of the twelve getting involved)

They've certainly liked to take this spin on things with the Zodiac, like in FFT. I wouldn't see it as an impossibility if they wanted to bring that in at some point.

[Bowen]

C.) There is either a thirteenth god or there is a parentage line missing (another of the twelve getting involved)

Fourteenth
Nald'Thal is both one god, and two gods. So the question is if there would be a fourteenth one. Sorry for the cherry-picking, but meh.

Anyways, I wouldn't assume anything about any relationships between the gods unless they were specifically stated. I think we all know how weird and complicated mythology/religion can get when it comes to this. (I'm looking at you, Greece.)