It's been a month and I've pinged on that upstream MR a couple of times, and three people have been mentioned. I haven't received any actual feedback on the fix when the bug is obvious and easily reproduced, and a Linux test case is attached.
I suspect that GNOME is simply not interested in fixing their X11 bugs, and I don't see another option than working around it on our side, so reopening this.
I don't think the workaround is so bad, windows will all have override-redirect set from their creation in unmanaged mode, and only managed mode will change and override-redirect will be set only for windows that need it, right after they have been created.