its intentionally drawn by the the theme

We could perhaps do with just using $bg_color and no border though.

this is not intentionally drawn by the theme, those borders should't be there:

.scrollbars-junction { // the small square between two scrollbars
  border-color: transparent;
  background-color: darken($bg_color, 5%);
  &:backdrop { background-color: transparent; }
}

P.S. Trinh Anh Ngoc, you're doing us a great service spotting all those issue, keep up the work!

Finally we figured out what that was, fix pushed to master and 3.14 branch