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.