I found how to make Knossos look native on Ubuntu (with Unity), or any GTK3 window manager ! Not exactly easy, though, because Qt uses GTK2 themes, while some of the widget styles we need are found in GTK3...
1) The window has to be borderless (we have to get rid of the 9px margins around "centralwidget"). It will probably look better on OS X, and Windows adds its own window borders anyway !
2) The Horizontal Layout which contains "settingsButton", "listControls", "pageControls" and a horizontal spacer has to be converted to a QFrame. By default, that will not change anything on other platforms.
3) Now, If we detect a GTK3 WM (Unity or Gnome-shell) with a known theme (having Gnome-shell default theme, Radiance and Ambiance would be good enough), we load a Qt CSS stylesheet and apply it to the QFrame to mimic GTK3 "Primary Toolbar" widget.
I'm still searching for the most simple and reliable way to detect the theme in 3). I'm also searching for the exact CSS values I need, and GTK3 themes are not exactly the easiest kind of CSS to read.
EDIT : Nailed it ! I have a Qt style sheet that gives Knossos a native look on Ubuntu's default Ambiance theme. (see 2nd screenshot)
EDIT 2 : Updated to Symfony 2.5.6 and latest FoSUB... I had to fix user management because they made some changes to their namespaces, and moved classes around...
[attachment kidnapped by pirates]