Let's see if I can explain myself properly, better with an image:
Nautlius example
I want to create a folder, and the pop up dialog appears. If by any reason I want to see the files behind, I can't move the small window, the main window of the app moves instead. I tried pressing Alt, Shift, Super Key or Ctrl + click and no results. I find it a very annoying feature of Gnome. For this example might seem silly, but for apps like QGIS with a lot of opening windows is very troubling.