Why are DIVs in the wrong order in Zen theme
I'd guess it has mainly to do with SEO.

From SEO Tutorial:


  In the HTML code for the page, the body text should be as close to the
  beginning of the code as possible, because there is a limit to how far
  down into a page a search engine spider will go to try to find text.
  So make sure your text comes before some really long JavaScript menu
  in the code for the page, or else the search engine won't make it far
  enough into the page to index the text. The search engine spider may
  never see the text if it is buried way down at the end of the code.


From 27 Quick Tips to Top Search Engine Rankings:


  
  If you have a persistent (on most or all of your pages) navigation bar at the side of each page, your table is almost certainly set up in
  such a way that it pushes your page's body text down the HTML
  document. Search engines give prominence to keywords nearer the
  beginning of a HTML document. So, design your HTML table so that the
  navigation bar is placed after your main body text.