This is not hard to defeat
Advertisers would have to jump a few more hoops but I doubt it's *that* hard for them to change the JS boiler plate they supply to hosting sites to inject their ads. Javascript can read and write cookies from its own origin so the glue the advertiser supplies could read the cookie from the host's origin, slap it onto the url request for the ad, and then update the cookie again in the host based on the response.
And that's just on the client side. Advertisers could provide modules for PHP, Java, Apache which injects the tracking cookies from the host domain in the request so there is no way to tell it apart from other cookies the site might issue.
Then there's storing data in flash shared objects, silverlight storage, HTML 5 storage and a raft of other places. See Evercookie for the ways this could be done. Basically if an advertiser wanted to track you they will.