mako appears with scale=1, and finds the output prefers scale=2, so it redraws with scale=2. This makes the window reshapes (supposingly because pango redraws with higher dpi and the rounding is different). So every time it appears, it flickers once.
Proposed solution
Remember last scale because it's very likely that the next time a notification is shown it's on the same output, thus avoiding above flickering in this case.
The problem
mako appears with scale=1, and finds the output prefers scale=2, so it redraws with scale=2. This makes the window reshapes (supposingly because pango redraws with higher dpi and the rounding is different). So every time it appears, it flickers once.
Proposed solution
Remember last scale because it's very likely that the next time a notification is shown it's on the same output, thus avoiding above flickering in this case.