I have to admit that I don't know the lore arround gods enough, but being able to choose between 2 domain if that's necessary for her story is fine to me.
It's better than no choice and it's still customization even if it's limited.
This could be a great way to "respec" while keeping everything that is story related safe.
Such customization before the beginning of the game would also avoid the non sense "respec mirror" (from a RP point of view)
You may still get a chance to switch her to Life. I suspect Shadowheart was a priestess of Selune but was brainwashed to become a worshipper of Shar. That I suspect is her big secret.
At any rate I agree with you. I wish we can customize our origin companions as much as possible before starting the game.