Off the top of my head I can't remember for sure why we don't put the top script in the head but I do seem to remember there was a reason. They only say it is ideal to have it in the head not required.
Generally I recommend the html file upload way of verifying webmaster tools. That way it is independent of needing a (meaningless) meta tag in the layout.master file which you may forget if you make a new skin or use more than one skin on your site or have any static html pages in your site that are not part of mojoPortal. It also makes the verification almost immediate.
Hope that helps,
Joe