John Yates
From the xmonad FAQ and some googling I believe that when that window appears I need to set its override-redirect attribute to true and define it as a strut. Though I am working my way through Hal Daumé's "Yet Another Haskell Tutorial" I fear it may be a while before I can code such a doStrut function. Thus my appeal to the readers of this list. My sense is that when the mini-buffer window appears it is properly sized and positioned. Thus there should be no need to compute the strut components, they should be directly liftable from the window.
I don't know whether this is the best approach, but it occurs to me that having the mini-buffer frame declare itself as a strut (by setting _NET_WM_STRUT_PARTIAL) might be a good way to do it? There's an xmonad extension to handle struts, and presumably other window managers could make use of it, too. (I don't know whether this could be done in elisp. Hmm, I guess it's not, but that feels like a logical thing for Emacs to be able to do, so maybe add a frame parameter to do that?)