I haven't seen explicit documentation about the rewriting behavior, but I assumed they were rewriting on based on the before and after waterfall charts in this blog post[1]. I agree it's not a great idea. Cloudflare actually recommends blacklisting problematic scripts [2], which partially defeats the feature's usefulness.

  [1] http://blog.cloudflare.com/56590463
  [2] http://www.cloudflare.com/wiki/Rocket_Loader