When you say out of shape, I assume you mean out of condition, and it seems as if that's true. Clearly she hasn't had time or ability to train in the way that she would need to, which seems mostly to be a reflection of her injury/injuries. The lack of back flexibility is something we've seen for awhile, and for years it's been known that she has some kind of back problem, either chronic or recurrent. Yes, she used to have a lovely layback, and an especially fine spreadeagle. I'm sorry to see that those elements are no longer at her best.
It's hard to judge her musicality. It was excellent when she was fourteen or so, and I don't think that's something that you lose. So what she has lost is completeness of execution--extension, posture, placement. This time out, however, her jumps looked solid, though not spectacular.
I have heard time and time again that Rachael is a lot more impressive when seen live. I don't know what that means in terms of whether speed, lift, and so on show up better in a live setting. I just know that this particular long program wasn't as distressing to watch on YouTube as I feared it could be. In fact, many elements of her program looked pretty good.