Check the attached screenshot, web inspector shows the right element size and position, but Safari renders it in a wrong place. The element reacts on mouse events also correctly - according to its real position.
Here you can find the live example https://3dflipbook.net/css-layer-highlight
This is a regression issue, it was working fine in 15.6.
Bug tracker: https://bugs.webkit.org/show_bug.cgi?id=278898
Please fix the issue.