Arguably, having the menu visible is not the default setup, is it? The default fold-out "Firefox" menu simply doesn't have that issue and is not transparent.
I agree it's a problem in Thunderbird, which has a menu by default.
I think that if you try to tweak Firefox 4+ to look like 3.6 you're going to run into suboptimalities. It evolved. I think that if you get used to the changes, they're actually changes for the better (new menu giving more vertical room, tabs-on-top, etc).
Here is a screenshot comparing FF 3.5 to 4: http://cache.gawker.com/assets/images/4/2009/12/500x_firefox...
(3.5 is right)