It might be two bugs related or just one bug (or again one non-Qt issue and one Qt-bug)
Just launch Window Flags example provided by Qt to reproduce it.
- click on WindowStaysOnTop => The Gnome dock stays on top (see image 1)
- click on X11ByPassWindowManager => the window is now on top, but for the part of the window that is above the dock, you can't click on buttons etc (the events won't be triggered I presume)
On blue the gnome dock, on red the part where no interaction is possible