I have to admit, I was heartbroken to find that the paddles were not unique. I've started a petition in the Xbox feedback section, where people can vote for things they want.
However, I truly love using the Elite controller for ED. I keep the paddles mapped to XABY, and set them for throttle and lateral thrusters.
All the buttons that were mapped to XABY have been rebound to a combination of shoulder buttons and thumbsticks. I easily prefer this over a HOTAS. It's perfect for me, and I never would have used this set up if the paddles were unique. They still need to be though!
Edit: Oh, and I actually have room for every single command that's needed. Even the select next star sytem waypoint, which is so useful. Of course, you can do this with any setup, but it feels more natural working off the shoulder buttons.
Also, I can't remap the start or back button... lame lol
Edit Edit: I'm not sure if I'm seeing your bindings correctly. Are your thrusters bound to buttons that need to be combo pressed to perform actions? I went that route originally but found it to be extremely lacking, due to potentially activating a function on accident, during battle.