From the comments: "The short answer is that the third-party provider must make small modifications to take advantage of LightningJS. This is done by adding the bootstrap Javascript and ensuring that the code uses window.parent for manipulation of the original document." That's kinda a big asterisks to add. That said, deferring JS safely is really hard. It's not a bad thing for more people to be working on.
I agree. LightningJS was originally written for third-party Javascript providers to improve their own embed code, though I think it would be awesome if end-users could easily take matters into their own hands. Maybe something for future development...