I just want to mention that I have the same positioning issues with
xrandr and not twinview.

Previously, with my screens stacked vertically (smaller screen above a
larger one), the notifications would appear (I believe) in the top-right
corner of the virtual display, which was a non-visible section.

Re-arranging the screens side-by-side 'fixes' things, but at the cost of
3d acceleration (the virtual display is now greater than my card's
2048x2048 limit).

@jcornwall -- perhaps having the bubbles grow upward from the bottom
would be simpler than trying to change the positioning logic?

-- 
regression vs. notification-daemon: positioning when multiple screens are 
available
https://bugs.launchpad.net/bugs/331369
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