I suspect this has to do with the change Apple made around the iOS 12.2 timeframe, where when a phone is rotated to portrait, the URL bar shrinks and the navigation bar is hidden. But when you rotate it back to portrait, an empty white area appears at the bottom of the screen, and there doesn't appear to be a way to make it go away.
If you rotate the device to landscape then it resizes and the div still fills the screen. If you load even a very simple web page into Safari that contains a div with a 100% height, then the result is correct and you get a full-screen div. I've observed some strange behavior that started around iOS 12.2 and continues through iOS 13.x.
