Sometimes compromises must be made to meet this requirement.
I am not against doing a compromise (though I don't like the final look that you will have when you use add_theme_page for so many options). I was just questioning its inclusion as a requirement for version 3.0.4 as opposed to 3.1 as agreed in the reviewers' discussion.
A separate location for the theme options group is confusing, especially if it's alone at the end of the menu
That's really a question of taste and organization. If you look at the commercial theme marketplace you will see several themes with a separate section, and not necessarily for branding - some themes do a lot more stuff than others. At the end of the day all talk of "confusion" is a one-time thing for most users. After all people do adapt to plug-ins that introduce new menu items (e.g. GD Star Ratings)
If another child theme/plugin/component/extension claims the position of that top menu item, either yours or the other one is gone, how's that for usability?
If you add a menu item without a position argument it gets added to the bottom of the menu, and any number of themes or plugins could use a blank argument - they just would get stacked at the bottom of the menu one after the another. While I cannot control where someone else puts his/her menu, I surely can add mine using a blank position argument - that way I don't take anybody else's position and somebody else doesn't take mine due to a conflicting position argument. This to me is a non-issue.