if you ignore a window other windows will be positioned on top of it if you do not reserve the space. and the issue is how to get them back to the front and instantanously get them back without inserting gaps into the layout for a short period of time (as thats rather slow in some cases).
Well for me, it was on top. I guess that depends on window parameters. Check dzen options or command-line tools that might set always-on-top or similar.
same problem from the command line. as one used doIgnore, the window isnt managed anymore and thus does not appear in the output of wmctrl -l. so receiving the windowid is the problem here again.
That might be because wmctrl talks to window manager, and xmonad says "I don't know such window!". You could search for other command-line tools.