I just find out there is a bug in xorg-core (nothing to do with mesa
directly), that breaks the “transparency” because
compositors do not know how to handle blending on sRGB visuals.
The patch will be in xorg 1.19.7 (and thus in bionic), but not in artful or xenial (AFAIK).
I just sent a patched xorg-core to padoka ppa and after some testing,
if all goes well, im gonna send it to padoka stable as well.