See also: https://github.com/WordPress/gutenberg/issues/14878
In my case the bug only presents when I have scrollbars set to always show in OS X, as described in that GiHub issue. When scrollbars are set to show “Automatically based on mouse or trackpad” there is no flickering.
Until the fix finds its way into WP core that might be a workaround if you are on OS X.
