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Hm the modified patch you've posted here seems like it is broken according to wm specs; the issue is that the window should be waiting for the wm to configure it once it is shown, but you've subverted that by toggling the configured flag if the environment is a compositing wm (and added a roundtrip to every event).
I'm testing here with the latest EFL from master (rEFL3932c6838292472b14f6dcfd90e74c59554c9524) and this patch applied on top: things seem to work as expected in Enlightenment 0.23 as well as other WMs. I'm wondering if this is an issue with the 1.22 branch somehow...
Hm after quite some time looking into this, I've run out of time. There's some sort of X11 protocol handling race condition which triggers under enlightenment/efl in 1.22 but is resolved in 1.23. I'll skip backporting this, but it does seem to fix the issue in 1.23.