A real test, I think, would take some time and effort to conduct.
I don't think it's enough to put up two pages to test navigation placement, for example, because it is the consistency
of navigation that helps a search engine differentiate between links that are content and links that are navigation. Give me six web pages using the same template and I can write a program in thirty minutes that will separate [url=http://searchengineland.com/070531-115312.php]Real[i][/i] Content[/url] from systemic elements like header, footer, and navigation. Give me only two pages, using two different templates, however, and my program would be lost.
I believe the placement of words within the content is important in determining relevancy for the same reason your ninth grade English teacher taught you to write a topic sentence for each of your papers. Good writers are going to do that any way. I also believe, however, that today's search engines are VERY good at paring content from supporting structure. Just like your teacher, the engines generally know
where to look for that topic sentence.
It's going to take a lot more empirical evidence than simply two web pages to prove anything useful, though. Heck, we already know one has to rank higher than the other even if both are identically relevant, so the first test is just like flipping a coin to see if it comes up heads or tails. One flip, however, isn't going to tell you if the coin is weighted to always land the same.
<edit>I was still typing, it would seem, while Jill said much the same.