The new global "Keep panel below windows" option, in the GNOME control center / Desktop / Panel / Miscellaneous tab, mixes very badly with panels that either auto-hide or explicitly hide. When you make a panel hideable, it's because you want to use that screen real estate for windows most of the time, but have the panel pop out on top of them when you unhide it. I can see that the property might be OK for panels that are present all the time, since then it lets you put another window over the panel temporarily and move it out of the way when you need the panel. However, it should not be global; it should be per-panel and should be available to turn on/off from the same dialog(s) where you can turn autohiding and the hide buttons on/off. I found it very confusing that the option is new, global, on by default, and somewhat hard to find.
Seems sensible, I'll forward the bug to the panel maintainers.
I guess I'd go so far as to say that nearly all the options in the panel config dialog are evil. ;-) We aren't really willing to diverge from upstream maintainer on this though, so I'm going to close the bug here and leave it up to http://bugzilla.gnome.org.