Hi, I'm the Chromium dev from the linked bug (and also a contributor to Enlightenment about 12 or 13 years ago -- hi!).

From the log in comment #21 at the Chromium issue, it appears to me that _NET_CLIENT_LIST_STACKING contains the IDs of windows created by E (0x80015e, 0x800039, 0x800041) rather than the actual client windows further down the tree (0xa00004, 0xe000c9, 0x1800003).  Per http://standards.freedesktop.org/wm-spec/wm-spec-1.3.html#id2687686 and the behavior of other window managers that I've checked, I believe that it should contain the client windows' IDs instead.  Am I mistaken?