BioWare is good at providing the illusion of choice. They did it in KotOR, and they're doing it here. We're all playing the same narrative - it's how that narrative plays out that differs. Nothing significantly changed the game story in KotOR, either.
Not really. I haven't played all of the stories but I haven't seen a point yet where what you do significantly changes the game story. You might have bits where it's 'Oh no, that's not nice/good!' But then that is soon forgotten. Presumably because it would've been too hard to track multiple plot lines with 8 stories.
I didn't know that about the companions in beta. Interesting. Shame that BW pulled that.