I will be charitable and call xmonad's floating layer support a hack.  And I think this is the oldest open bug in the bug tracker.  :(  There is a module that tries to make things saner (XMonad.Layout.TrackFloating) but it has some issues.

Unfortunately, this issue more or less demonstrates that the StackSet zipper at the heart of xmonad isn't quite good enough.  (And things get worse if you try to add support for other EWMH layers.)