To be honest, the choice reminded me a bit of this:
http://darksoulswiki.wikispaces.com/file/view/2037.png/273347994/2037.png
In the end, I am not sure if the inconsistency towards the end is actually a hint at action behind the scenes, or if it is just a fluke, an error, a genuine mistake or a tiny little excuse for the content that, alas, didn't make it in after all.
To my - current - best knowledge, the choice of necklace had no actual impact on the game beyond the Joakim Morgren hand. Besides, there are hints at the bird and the cage pretty much being the same thing anyway...
OT: The bird, as I don't like cages. Turns out I also but partially liked the bird. If the bird is out of the cage, does not the bird become a mobile form of a cage, protecting, but also limiting things quite harshly? In the end, of course, it's not a proper, pure asshole bird, but a useful tool of mass destruction.
Still, it feels like an über Big Daddy, still got sparkles of that old scare, but plain being too powerful to be any fun. Is the bird not just the illusion of freedom? Did Levine and friends feel too oppressed by the Big Daddies? Did the Big Sister thing turn out to be a major turn off for them? Did they want to just tear it all down?