I'm one step further: I got the pop up window to work. The trick is to move the mouse to the middle of the "multi commander" window, and then invoke the "Favorites" window using the hotkey which you have suggested, Alt-Backspace. I think the problem with the Favorites windows is that it is placed just centered on top of the main window, i.e. away from the star button. Since I have "autoraise" and "focus follows mouse" enabled (I don't switch windows by clicking into them, but by moving the mouse over the window which should receive the focus), the main window gets the focus again, before the mouse has a chance to reach the pop-up. I was lucky that the pop-up was a modal window! The real cause of the problem seems to be therefore, that the pop up window doesn't use the property "always in foreground", and hence can be hidden again.
Now there is one more problem left: I'm using the key combination Control-DIGIT to switch between virtual desktops. Is there a way to assign different key combinations to the favorites, for example Control-Shift-DIGIT?