iOS Safari scrolls down when interacting with video.js player

Safari on iOS (10.3) jumping (scrolls down) when closing video.js player popup menu by clicking on menu button the second time.

How to reproduce:

1. https://codepen.io/mkhazov/full/PjBJvb/. Open this pen in Safari on iPhone or xcode simulator.
2. Scroll down-up
3. Click on quality selection button
4. Click it again.

recorded video: http://www.screencast.com/t/IPkjEo2dxW7

It's definitely mobile Safari bug (there's no js code responsible for scroll), but I can't find the suitable workaround.

This can be fixed by following CSS as proposed here:

html,
body {
  height: 100%;
  -webkit-overflow-scrolling: touch;
  overflow: auto;
}

but it breaks other things (e.g. window.scrollY / $(window).scrollTop()) so I can't use it.

Any ideas/suggestions would be appreciated.