I actually think the WIRED piece [1] to which OP refers does a good job of addressing this point. In particular, the WIRED article mentions PORTAL, a competing device called the SafePlug (which we did some research on to show that it does this job rather poorly), and something I'd never previously heard of called OnionPi.

Also, the article states very clearly states: "If you use the same browser for your anonymous and normal Internet activities, for instance, websites can use “browser fingerprinting” techniques like cookies to identify you.", which is basically the point of this post.

The WIRED piece even goes further, offering the same solution as is offered in this piece: "[an expert] suggests that even when routing traffic over Tor with Anonabox, users should use the Tor Browser, a hardened browser that avoids those fingerprinting techniques."

So while I understand the gripe that a transparent Torifying proxy doesn't necessarily do what you think it should, I would also praise WIRED for doing a pretty good job of handling these difficult and subtle issues in their article about the Anonabox.

[1] http://www.wired.com/2014/10/tiny-box-can-anonymize-everythi...