This bug may belong to Metacity rather than the HIG; if so, apologies.

Throughout Gnome, Preferences windows are floating windows; they're not modal,
but they insist on staying above all other windows in the application. This
makes no sense. A window should float if it is very small and people often need
to switch between it and other windows (for example, toolboxes and palettes).
Preferences windows do not fall into this category. Because they're
instant-apply windows rather than dialogs, people can close them at their
leisure, so should be able to (for example) raise document windows above them.