Yes, it's making more sense now, thanks to your explanations. This, in particular, is what I was looking for — the because part — since the "because" speaks to the "why" and the "how" of her free agency:

But because of all this manipulation, all this deliberate writing of her, she has the strength and the tools for breaking free and write her own story.

I looked at this and started to wonder about how all the manipulation would make her stronger, and then I thought about two things. First, the engineering term "testing to destruction," in which engineers test the true strength of materials by forcing them through enough stress that they break, noting that point, and recreating the materials to withstand that amount of stress. River has certainly been tested to destruction in ways no one else has, both within the Whoniverse and in our own universe.

Secondly, I thought of how swords are tempered by fire into final strength, hardness and sharpness — and how glass is formed by fire into things both beautiful and strange, opaque and transparent, clear and many-colored, and that, too, is a tempering, although what is tempered is as fragile as a human heart and soul. And that, too, is River.

So, yeah, you're making all the sense in the world! Thanks so much for taking the time to explain; it's one of the many reasons I love your commentaries — you interact with your readers, and you give them something about which they want to interact.

Also, here's what I wrote about TGWW, if you're interested.