nalenb, thanks for the time you spent looking at this. A lot of your issues are because this is a work in progress. Initially we are giving it the exact same look and feel as the windows versions, knowing that it won't be a good Mac UI citizen, but it does make the design easy. We intend to then make it conform to the Mac UI guidelines.
We have talked about using drawers like Mail, but the current system does match what Safari does with the Bookmarks. We all agree about the "tab happy" preferences and are discussing options for that.
All of you comments and suggests will be considered as the design moves forward.