I don't have a precise way do to that, but it still looks like something to fix in winex11 if it doesn't work, rather than in explorer.exe. Using SWP_NOZORDER on windows is enough to make sure the window isn't raised.
There are ways with X11 to map a window without activating (EWMH documents how _NET_WM_USER_TIME should be set to 0 prior to mapping it), and perhaps without raising it, or some other way to restack the windows correctly, we should use them.
Of course, this is the long way because of how bad winex11 still is at keeping states consistent with the client/host but hopefully that can be improved.