Actually, the graphs did not entirely match what I expected to see. I expected far more concordance between the US and Australia, the US and Japan, and Australia and New Zealand than what I actually saw. I wrote the analysis after generating the graphs in an attempt to explain what I was seeing. FWIW, one of the reasons I did this was to contribute something to the discussion of the TPP that was actually based on data, rather than just a general "feel" one gets after reading the leaked text.
I did note in the article that Japan appears to be just as isolated. But I don't know how Japanese businesses influence their government nearly as well as how I know US businesses influence the U.S. Trade Representative, so I didn't focus on that in the article.
As for the Peru/Chile statement, I called such connections "natural" based primarily on geographical proximity or shared languages. I think it's entirely reasonable to expect more overlap of positions in an international trade negotiation between countries on the same continent, speaking the same language, than between far-flung continents with totally different languages. Such a connection doesn't mean anything more than that the countries agree on an issue in the text.