Hard bug to explain and still not sure what is going on. This only happens in iOS Safari.
This page has a composited layer (the green one) and an absolutely positioned element behind it. When the page is refreshed you'll see the red element flash before the green one renders again.
So I think it's to do with the fact that the green element is cleaned up quite quickly and the red hangs around until the document is destroyed on refresh.
But...if I change the red layer to position: fixed this issue goes away, so I'm not really sure what's going on?
Confirmed this is a bug in iOS safari where composited layers are cleaned up faster than non-composited layers.
See same test case but red element has fixed position.
A quick fix would be to also lift that layer to the GPU via the null transform hack by applying
transform: translateZ(0) to the element that is flashing.